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(-) Description

Title :  CRYSTAL STRUCTURE OF LRP6-DKK1 COMPLEX
 
Authors :  Z. Cheng, W. Xu
Date :  31 May 11  (Deposition) - 26 Oct 11  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,X
Biol. Unit 1:  A,X  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Wnt, Receptor, Lrp5, Lrp6, Ldl Receptor-Like Protein, Dickkopf (Dkk), Ywtd B-Propeller, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Z. Cheng, T. Biechele, Z. Wei, S. Morrone, R. T. Moon, L. Wang, W. Xu
Crystal Structures Of The Extracellular Domain Of Lrp6 And Its Complex With Dkk1.
Nat. Struct. Mol. Biol. V. 18 1204 2011
PubMed-ID: 21984209  |  Reference-DOI: 10.1038/NSMB.2139

(-) Compounds

Molecule 1 - LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6
    ChainsA, B
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System PlasmidPACGP67B
    Expression System Taxid7108
    Expression System Vector TypePLASMID
    FragmentE3E4, RESIDUES 629-1243
    GeneLRP6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLRP-6
 
Molecule 2 - DICKKOPF-RELATED PROTEIN 1
    ChainsX
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET32M
    Expression System StrainBL-21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    FragmentDKK1C, RESIDUES 184-266
    GeneDKK1, UNQ492/PRO1008
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDICKKOPF-1, DKK-1, HDKK-1, SK

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABX
Biological Unit 1 (1x)A X
Biological Unit 2 (1x) B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3S8V)

(-) Sites  (0, 0)

(no "Site" information available for 3S8V)

(-) SS Bonds  (17, 17)

Asymmetric Unit
No.Residues
1A:893 -A:904
2A:900 -A:914
3A:916 -A:929
4A:1207 -A:1218
5A:1214 -A:1228
6A:1230 -A:1243
7B:893 -B:904
8B:900 -B:914
9B:916 -B:929
10B:1207 -B:1218
11B:1214 -B:1228
12B:1230 -B:1243
13X:189 -X:201
14X:195 -X:210
15X:200 -X:237
16X:220 -X:245
17X:239 -X:263

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3S8V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030350S817CLRP6_HUMANPolymorphism2302686A/BS817C
2UniProtVAR_024520V1062ILRP6_HUMANPolymorphism2302685A/BI1062I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030350S817CLRP6_HUMANPolymorphism2302686AS817C
2UniProtVAR_024520V1062ILRP6_HUMANPolymorphism2302685AI1062I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_030350S817CLRP6_HUMANPolymorphism2302686BS817C
2UniProtVAR_024520V1062ILRP6_HUMANPolymorphism2302685BI1062I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 20)

Asymmetric Unit (1, 20)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LDLRBPS51120 LDL-receptor class B (LDLRB) repeat profile.LRP6_HUMAN63-106
107-149
150-193
194-236
372-414
415-457
458-501
502-544
545-584
674-716
 
717-759
 
760-802
 
843-885
 
803-839
 
977-1025
 
1026-1068
 
1069-1113
 
1114-1156
 
1157-1198
 
  20-
-
-
-
-
-
-
-
-
A:674-716
B:674-716
A:717-759
B:717-759
A:760-802
B:760-802
A:843-885
B:843-885
A:803-839
B:803-839
A:977-1025
B:977-1025
A:1026-1068
B:1026-1068
A:1069-1113
B:1069-1113
A:1114-1156
B:1114-1156
A:1157-1198
B:1157-1198
Biological Unit 1 (1, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LDLRBPS51120 LDL-receptor class B (LDLRB) repeat profile.LRP6_HUMAN63-106
107-149
150-193
194-236
372-414
415-457
458-501
502-544
545-584
674-716
 
717-759
 
760-802
 
843-885
 
803-839
 
977-1025
 
1026-1068
 
1069-1113
 
1114-1156
 
1157-1198
 
  10-
-
-
-
-
-
-
-
-
A:674-716
-
A:717-759
-
A:760-802
-
A:843-885
-
A:803-839
-
A:977-1025
-
A:1026-1068
-
A:1069-1113
-
A:1114-1156
-
A:1157-1198
-
Biological Unit 2 (1, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LDLRBPS51120 LDL-receptor class B (LDLRB) repeat profile.LRP6_HUMAN63-106
107-149
150-193
194-236
372-414
415-457
458-501
502-544
545-584
674-716
 
717-759
 
760-802
 
843-885
 
803-839
 
977-1025
 
1026-1068
 
1069-1113
 
1114-1156
 
1157-1198
 
  10-
-
-
-
-
-
-
-
-
-
B:674-716
-
B:717-759
-
B:760-802
-
B:843-885
-
B:803-839
-
B:977-1025
-
B:1026-1068
-
B:1069-1113
-
B:1114-1156
-
B:1157-1198

(-) Exons   (0, 0)

(no "Exon" information available for 3S8V)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:600
 aligned with LRP6_HUMAN | O75581 from UniProtKB/Swiss-Prot  Length:1613

    Alignment length:615
                                   638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928       938       948       958       968       978       988       998      1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238     
          LRP6_HUMAN    629 VPEAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIRKAQEDGSQGFTVVVSSVPSQNLEIQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGVVLKGEQDRPRAVVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKIDMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSCPMHLVLLQDELSC 1243
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeeee......eee........eeeeeee....eeeeee....eeeeee......eeee........eeeee....eeeeee....eeeeee......eeee......eeeeeee....eeeeee.....eeeeee......eeee.........eee....eeeeee....eeeeee......eeee.....eeeeee...eeeeee....eeeeee.......eeee......eeeeee........hhhhhhhhhh..eeee..--.eeee.....ee......ee....eeeee....eeeee....--..ee.......eeeeeeee....eeeeeee...eeeee.......eeee..--------..eeeeeee....eeeeee....eeeeee....eeeeee......eeeeeee....eeeeee......eeeeee......eeee......eeeeeee....eeeeee....eeeeee......eeee......eeeeee...eeeeee....eeeeee.---...eeee.......eeeee...hhhhhhh....hhhhhh..ee.........ee.............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------LDLRB  PDB: A:674-716 UniProt: 674-716     LDLRB  PDB: A:717-759 UniProt: 717-759     LDLRB  PDB: A:760-802 UniProt: 760-802     LDLRB  PDB: A:803-839                ---LDLRB  PDB: A:843-885 UniProt: 843-885     -------------------------------------------------------------------------------------------LDLRB  PDB: A:977-1025 UniProt: 977-1025         LDLRB  PDB: A:1026-1068 UniProt: 1026-1068 LDLRB  PDB: A:1069-1113 UniProt: 1069-1113   LDLRB  PDB: A:1114-1156 UniProt: 1114-1156 LDLRB  PDB: A:1157-1198 UniProt: 1157-1198--------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3s8v A  629 VPEAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVP--GFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVIDEQ--PDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIRKAQEDGSQGFTVVVS--------IQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGVVLKGEQDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKIDM---EGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSCPMHLVLLQDELSC 1243
                                   638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828       838       848       858       868       878       888       898       908  |    918       928       938       948   |  |958       968       978       988       998      |  -     |1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168   |  1178      1188      1198      1208      1218      1228      1238     
                                                                                                                                                                                                                                                                                                                 908  |                                      952  |                                              1005     1014                                                                                                                                                          1172   |                                                                   
                                                                                                                                                                                                                                                                                                                    911                                         955                                                                                                                                                                                                                         1176                                                                   

Chain B from PDB  Type:PROTEIN  Length:604
 aligned with LRP6_HUMAN | O75581 from UniProtKB/Swiss-Prot  Length:1613

    Alignment length:613
                                   640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240   
          LRP6_HUMAN    631 EAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIRKAQEDGSQGFTVVVSSVPSQNLEIQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGVVLKGEQDRPRAVVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKIDMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSCPMHLVLLQDELSC 1243
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eeeee......eee........eeeeeee....eeeeee....eeeeee......eeee........eeeee....eeeeee....eeeeee......eeee......eeeeeee....eeeeee.....eeeeee......eeee.........eee....eeeeee....eeeeee......eeee.....eeeeee...eeeeee....eeeeee.......eeee........eeee........hhhhhhhhhh..eeee.....eeee.....ee......ee....eeeeee..eeeee.........ee........eeeeeee....eeeeee....eeeee.......eeee.---------..eeeeeee....eeeeee....eeeeee....eeeeeee.....eeeeeee....eeeeeeee..eeeeeeee......eeee......eeeeeee....eeeeee....eeeeee......eeee......eeeeee...eeeeee....eeeeee.......eeee.....eeeeeee...hhhhhhh....hhhhhh..eeee.....eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------I------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------LDLRB  PDB: B:674-716 UniProt: 674-716     LDLRB  PDB: B:717-759 UniProt: 717-759     LDLRB  PDB: B:760-802 UniProt: 760-802     LDLRB  PDB: B:803-839                ---LDLRB  PDB: B:843-885 UniProt: 843-885     -------------------------------------------------------------------------------------------LDLRB  PDB: B:977-1025 UniProt: 977-1025         LDLRB  PDB: B:1026-1068 UniProt: 1026-1068 LDLRB  PDB: B:1069-1113 UniProt: 1069-1113   LDLRB  PDB: B:1114-1156 UniProt: 1114-1156 LDLRB  PDB: B:1157-1198 UniProt: 1157-1198--------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3s8v B  631 EAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIRKAQEDGSQGFTVVV---------IQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGVVLKGEQDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKIDMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSCPMHLVLLQDELSC 1243
                                   640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000   |     -   |  1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240   
                                                                                                                                                                                                                                                                                                                                                                                                              1004      1014                                                                                                                                                                                                                                     

Chain X from PDB  Type:PROTEIN  Length:73
 aligned with DKK1_HUMAN | O94907 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:82
                                   193       203       213       223       233       243       253       263  
          DKK1_HUMAN    184 QEGSVCLRSSDCASGLCCARHFWSKICKPVLKEGQVCTKHRRKGSHGLEIFQRCYCGEGLSCRIQKDHHQASNSSRLHTCQR  265
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhh...eeeeee..eeeeee..............hhhhhh...........eeee.---------...eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                3s8v X  184 QEGSVCLRSSDCASGLCCARHFWSKICKPVLKEGQVCTKHRRKGSHGLEIFQRCYCGEGLSCRIQ---------SRLHTCQR  265
                                   193       203       213       223       233       243    |    -    |  263  
                                                                                          248       258       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3S8V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3S8V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3S8V)

(-) Gene Ontology  (117, 126)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (LRP6_HUMAN | O75581)
molecular function
    GO:0042813    Wnt-activated receptor activity    Combining with a Wnt protein and transmitting the signal across the plasma membrane to initiate a change in cell activity.
    GO:0017147    Wnt-protein binding    Interacting selectively and non-covalently with Wnt-protein, a secreted growth factor involved in signaling.
    GO:0034185    apolipoprotein binding    Interacting selectively and non-covalently with an apolipoprotein, the protein component of a lipoprotein complex.
    GO:0071936    coreceptor activity involved in Wnt signaling pathway    In cooperation with a primary Wnt receptor, initiating a change in cell activity through the Wnt signaling pathway.
    GO:1904928    coreceptor activity involved in canonical Wnt signaling pathway    Any coreceptor activity that is involved in a canonical Wnt signaling pathway.
    GO:0005109    frizzled binding    Interacting selectively and non-covalently with the frizzled (fz) receptor.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0019210    kinase inhibitor activity    Stops, prevents or reduces the activity of a kinase, an enzyme which catalyzes of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0005041    low-density lipoprotein receptor activity    Combining with a low-density lipoprotein particle and delivering the low-density lipoprotein into the cell via endocytosis.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0019534    toxin transporter activity    Enables the directed movement of a toxin into, out of or within a cell, or between cells. A toxin is a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0044332    Wnt signaling pathway involved in dorsal/ventral axis specification    The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell contributing to the establishment, maintenance and elaboration of the dorsal/ventral axis.
    GO:1904953    Wnt signaling pathway involved in midbrain dopaminergic neuron differentiation    Any Wnt signaling pathway that is involved in midbrain dopaminergic neuron differentiation.
    GO:0090244    Wnt signaling pathway involved in somitogenesis    The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state that contributes to somitogenesis.
    GO:0090245    axis elongation involved in somitogenesis    The developmental growth that results in the elongation of the rostral-caudal axis that contributes to somitogenesis.
    GO:1904886    beta-catenin destruction complex disassembly    The disaggregation of a beta-catenin destruction complex into its constituent components.
    GO:0060070    canonical Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes. In this pathway, the activated receptor signals via downstream effectors that result in the inhibition of beta-catenin phosphorylation, thereby preventing degradation of beta-catenin. Stabilized beta-catenin can then accumulate and travel to the nucleus to trigger changes in transcription of target genes.
    GO:0044335    canonical Wnt signaling pathway involved in neural crest cell differentiation    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes involved in neural crest cell differentiation.
    GO:0044340    canonical Wnt signaling pathway involved in regulation of cell proliferation    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes that contributes to modulating the rate or frequency of cell proliferation.
    GO:0071397    cellular response to cholesterol    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cholesterol stimulus.
    GO:0021587    cerebellum morphogenesis    The process in which the anatomical structure of the cerebellum is generated and organized. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. The cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
    GO:0021987    cerebral cortex development    The progression of the cerebral cortex over time from its initial formation until its mature state. The cerebral cortex is the outer layered region of the telencephalon.
    GO:0007268    chemical synaptic transmission    The vesicular release of classical neurotransmitter molecules from a presynapse, across a chemical synapse, the subsequent activation of neurotransmitter receptors at the postsynapse of a target cell (neuron, muscle, or secretory cell) and the effects of this activation on the postsynaptic membrane potential and ionic composition of the postsynaptic cytosol. This process encompasses both spontaneous and evoked release of neurotransmitter and all parts of synaptic vesicle exocytosis. Evoked transmission starts with the arrival of an action potential at the presynapse.
    GO:0060026    convergent extension    The morphogenetic process in which an epithelium narrows along one axis and lengthens in a perpendicular axis.
    GO:0071542    dopaminergic neuron differentiation    The process in which a neuroblast acquires the specialized structural and functional features of a dopaminergic neuron, a neuron that secretes dopamine.
    GO:0009880    embryonic pattern specification    The process that results in the patterns of cell differentiation that will arise in an embryo.
    GO:0060059    embryonic retina morphogenesis in camera-type eye    The process in which the anatomical structure of the retina is generated and organized in a camera-type eye during the embryonic life stage.
    GO:0006897    endocytosis    A vesicle-mediated transport process in which cells take up external materials or membrane constituents by the invagination of a small region of the plasma membrane to form a new membrane-bounded vesicle.
    GO:0035261    external genitalia morphogenesis    The process in which the anatomical structures of the external genitalia are generated and organized. The external genitalia are the outer sex organs, such as the penis or vulva in mammals.
    GO:0060325    face morphogenesis    The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.
    GO:1904948    midbrain dopaminergic neuron differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a midbrain dopaminergic neuron.
    GO:0030917    midbrain-hindbrain boundary development    The process whose specific outcome is the progression of the midbrain-hindbrain boundary over time, from its formation to the mature structure. The midbrain-hindbrain domain of the embryonic brain is comprised of the mesencephalic vesicle and the first rhombencephalic vesicle at early somitogenesis stages.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0006469    negative regulation of protein kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
    GO:0001933    negative regulation of protein phosphorylation    Any process that stops, prevents or reduces the rate of addition of phosphate groups to amino acids within a protein.
    GO:0071901    negative regulation of protein serine/threonine kinase activity    Any process that decreases the rate, frequency, or extent of protein serine/threonine kinase activity.
    GO:0034392    negative regulation of smooth muscle cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of smooth muscle cell apoptotic process.
    GO:0014033    neural crest cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neural crest cell.
    GO:0014029    neural crest formation    The formation of the specialized region of ectoderm between the neural ectoderm (neural plate) and non-neural ectoderm. The neural crest gives rise to the neural crest cells that migrate away from this region as neural tube formation procedes.
    GO:0001843    neural tube closure    The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
    GO:0042475    odontogenesis of dentin-containing tooth    The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    GO:0003344    pericardium morphogenesis    The process in which the anatomical structure of the pericardium is generated and organized.
    GO:2000055    positive regulation of Wnt signaling pathway involved in dorsal/ventral axis specification    Any process that activates or increases the frequency, rate or extent of Wnt signaling pathway involved in dorsal/ventral axis specification.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0045787    positive regulation of cell cycle    Any process that activates or increases the rate or extent of progression through the cell cycle.
    GO:0007204    positive regulation of cytosolic calcium ion concentration    Any process that increases the concentration of calcium ions in the cytosol.
    GO:0051091    positive regulation of sequence-specific DNA binding transcription factor activity    Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0090009    primitive streak formation    The developmental process pertaining to the initial formation of the primitive streak from unspecified parts. The primitive streak is a ridge of cells running along the midline of the embryo where the mesoderm ingresses. It defines the anterior-posterior axis.
    GO:0072659    protein localization to plasma membrane    A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
    GO:0090118    receptor-mediated endocytosis involved in cholesterol transport    A receptor-mediated endocytosis process involved in intracellular cholesterol transport.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0043434    response to peptide hormone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a peptide hormone stimulus. A peptide hormone is any of a class of peptides that are secreted into the blood stream and have endocrine functions in living animals.
    GO:0016337    single organismal cell-cell adhesion    The attachment of one cell to another cell via adhesion molecules, where both cells are part of the same organism.
    GO:0021794    thalamus development    The process in which the thalamus changes over time, from its initial formation to its mature state.
    GO:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0060535    trachea cartilage morphogenesis    The process in which the anatomical structures of cartilage in the trachea are generated and organized.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:1990909    Wnt signalosome    A multiprotein protein complex containing membrane-localized Wnt receptors and cytosolic protein complexes, which is capable of transmitting the Wnt signal. Contains at least a Wnt protein, LRP5 or LRP6, a member of the Frizzled (Fz) family, Axin and and a Dishevelled (DVL) protein.
    GO:1990851    Wnt-Frizzled-LRP5/6 complex    A protein complex containing a secreted Wnt protein associated with its receptor, Frizzled (Fz), and co-receptor low density lipoprotein receptor-related protein 5 (LRP5) or LRP6.
    GO:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0043235    receptor complex    Any protein complex that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0045202    synapse    The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

Chain X   (DKK1_HUMAN | O94907)
molecular function
    GO:0039706    co-receptor binding    Interacting selectively and non-covalently with a coreceptor. A coreceptor acts in cooperation with a primary receptor to transmit a signal within the cell.
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0050750    low-density lipoprotein particle receptor binding    Interacting selectively and non-covalently with a low-density lipoprotein receptor.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0048019    receptor antagonist activity    Interacts with receptors to reduce the action of another ligand, the agonist.
    GO:0004871    signal transducer activity    Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0090244    Wnt signaling pathway involved in somitogenesis    The series of molecular signals initiated by binding of Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state that contributes to somitogenesis.
    GO:0000904    cell morphogenesis involved in differentiation    The change in form (cell shape and size) that occurs when relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history.
    GO:0030326    embryonic limb morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
    GO:0007492    endoderm development    The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
    GO:0001706    endoderm formation    The formation of the endoderm during gastrulation.
    GO:1900116    extracellular negative regulation of signal transduction    Any negative regulation of signal transduction that takes place in extracellular region.
    GO:0060325    face morphogenesis    The process in which the anatomical structures of the face are generated and organized. The face is the ventral division of the head.
    GO:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0001942    hair follicle development    The process whose specific outcome is the progression of the hair follicle over time, from its formation to the mature structure. A hair follicle is a tube-like opening in the epidermis where the hair shaft develops and into which the sebaceous glands open.
    GO:0060323    head morphogenesis    The process in which the anatomical structures of the head are generated and organized. The head is the anterior-most division of the body.
    GO:0001707    mesoderm formation    The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
    GO:1904693    midbrain morphogenesis    The developmental process by which a midbrain is generated and organized.
    GO:0061743    motor learning    Any process in which an organism acquires a novel neuromuscular action or movement as the result of experience.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0030514    negative regulation of BMP signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the BMP signaling pathway.
    GO:0030178    negative regulation of Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the Wnt signaling pathway.
    GO:1904723    negative regulation of Wnt-Frizzled-LRP5/6 complex assembly    Any process that stops, prevents or reduces the frequency, rate or extent of Wnt-Frizzled-LRP5/6 complex assembly.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:1901296    negative regulation of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment    Any process that stops, prevents or reduces the frequency, rate or extent of canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment.
    GO:2000726    negative regulation of cardiac muscle cell differentiation    Any process that stops, prevents or reduces the frequency, rate or extent of cardiac muscle cell differentiation.
    GO:0042662    negative regulation of mesodermal cell fate specification    Any process that stops, prevents, or reduces the frequency, rate or extent of mesoderm cell fate specification.
    GO:0060394    negative regulation of pathway-restricted SMAD protein phosphorylation    Any process that decreases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
    GO:0033137    negative regulation of peptidyl-serine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:0048642    negative regulation of skeletal muscle tissue development    Any process that stops, prevents, or reduces the frequency, rate or extent of skeletal muscle tissue development.
    GO:0051964    negative regulation of synapse assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of synapse assembly, the aggregation, arrangement and bonding together of a set of components to form a synapse.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0090082    positive regulation of heart induction by negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency or extent of canonical Wnt signaling pathway that positively regulates heart induction. Canonical Wnt signaling pathway involved in heart induction is the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0030111    regulation of Wnt signaling pathway    Any process that modulates the frequency, rate or extent of the activity of the Wnt signal transduction pathway.
    GO:1904338    regulation of dopaminergic neuron differentiation    Any process that modulates the frequency, rate or extent of dopaminergic neuron differentiation.
    GO:0042663    regulation of endodermal cell fate specification    Any process that mediates the specification of a cell into an endoderm cell.
    GO:0002090    regulation of receptor internalization    Any process that modulates the frequency, rate or extent of receptor internalization.
    GO:0050807    regulation of synapse organization    Any process that modulates the physical form of a synapse, the junction between a neuron and a target (neuron, muscle, or secretory cell).
    GO:0051966    regulation of synaptic transmission, glutamatergic    Any process that modulates the frequency, rate or extent of glutamatergic synaptic transmission, the process of communication from a neuron to another neuron across a synapse using the neurotransmitter glutamate.
    GO:0032526    response to retinoic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
cellular component
    GO:0031901    early endosome membrane    The lipid bilayer surrounding an early endosome.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  LRP6_HUMAN | O75581
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        DKK1_HUMAN | O949073s2k 3soq 5fww 5gje
        LRP6_HUMAN | O755813s2k 3s8z 3s94 3sob 3soq 3sov 4a0p 4dg6 4nm5 4nm7 5air 5fww 5gje

(-) Related Entries Specified in the PDB File

3s8z CRYSTAL STRUCTURE OF LRP6-E3E4
3s94 CRYSTAL STRUCTURE OF LRP6-E1E2