Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THREE-DIMENSIONAL RECONSTRUCTION OF HUMAN LRP6 ECTODOMAIN COMPLEXED WITH DKK1
 
Authors :  K. Matoba, E. Mihara, K. Tamura-Kawakami, H. Hirai, S. Thompson, K. Iwa J. Takagi
Date :  29 Jun 16  (Deposition) - 18 Jan 17  (Release) - 18 Jan 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  21.00
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Wnt Signaling, Wnt Co-Receptor, Lrp6, Glycoprotein, Antagonist, Dkk1, Conformational Change, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Matoba, E. Mihara, K. Tamura-Kawakami, N. Miyazaki, S. Maeda, H. Hirai, S. Thompson, K. Iwasaki, J. Takagi
Conformational Freedom Of The Lrp6 Ectodomain Is Regulated By N-Glycosylation And The Binding Of The Wnt Antagonist Dkk1
Cell Rep V. 18 32 2017
PubMed-ID: 28052259  |  Reference-DOI: 10.1016/J.CELREP.2016.12.017

(-) Compounds

Molecule 1 - LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6
    Chains: A
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Taxid: 10029
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 20-630
    Gene: LRP6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LRP-6
 
Molecule 2 - LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 631-1246
    Gene: LRP6
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LRP-6
 
Molecule 3 - DICKKOPF-RELATED PROTEIN 1
    Chains: C
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: DKK1, UNQ492/PRO1008
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HDKK-1,SK

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric/Biological Unit (4, 17)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2GOL1Ligand/IonGLYCEROL
3NAG13Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:169 , THR A:212 , HIS A:253 , ARG A:259binding site for residue PO4 A 707
02AC2SOFTWAREARG A:396 , LEU A:413 , NAG A:705binding site for residue PO4 A 708
03AC3SOFTWAREARG B:985binding site for residue GOL B 1309
04AC4SOFTWAREASN A:262 , ALA A:263 , THR A:264binding site for Poly-Saccharide residues NAG A 701 through NAG A 702 bound to ASN A 262
05AC5SOFTWAREARG A:412 , ASN A:414 , PO4 A:708 , HOH A:801binding site for Poly-Saccharide residues NAG A 705 through NAG A 706 bound to ASN A 414
06AC6SOFTWAREVAL A:464 , ASN A:467binding site for Poly-Saccharide residues NAG A 703 through NAG A 704 bound to ASN A 467
07AC7SOFTWAREASN B:674 , PHE B:690 , ASN B:692binding site for Poly-Saccharide residues NAG B 1301 through FUC B 1303 bound to ASN B 692
08AC8SOFTWAREASP B:843 , ASN B:859 , THR B:861 , SER B:862 , NAG B:1305binding site for Mono-Saccharide NAG B 1304 bound to ASN B 859
09AC9SOFTWAREASN B:865 , NAG B:1304binding site for Mono-Saccharide NAG B 1305 bound to ASN B 865
10AD1SOFTWAREALA B:924 , ASN B:926binding site for Mono-Saccharide NAG B 1306 bound to ASN B 926
11AD2SOFTWARETRP B:1030 , ASN B:1039 , THR B:1041 , GLY B:1045 , SER B:1047 , VAL B:1050binding site for Poly-Saccharide residues NAG B 1307 through NAG B 1308 bound to ASN B 1039

(-) SS Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1A:274 -A:289
2A:291 -A:304
3A:573 -A:584
4A:580 -A:593
5A:595 -A:608
6B:893 -B:904
7B:900 -B:914
8B:916 -B:929
9B:1207 -B:1218
10B:1214 -B:1228
11B:1230 -B:1243
12C:189 -C:201
13C:195 -C:210
14C:200 -C:237
15C:220 -C:245
16C:239 -C:263

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GJE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GJE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GJE)

(-) Exons   (0, 0)

(no "Exon" information available for 5GJE)

(-) Sequences/Alignments

Asymmetric/Biological 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:611
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeee..................eeeeeee....eeeeee....eeeeee......eeeee........eeeee....eeeeee....eeeeee......eeee......eeeeeee....eeeeee.....eeeeee......eeee......eeeeeee....eeeeee......eeee......ee...........eee...eeeeee....eeeeee...................eee.hhhhh................eeee......eeee...................eeeeeee...eeeee..........ee......eeeeeee....eeeeee....eeeee.......eeee........eeeee....eeeeee....eeeeee......eeeee....eeeeeeee....eeeeeee....eeeeee......eeee......eeee..hhhhh...eee....eeee........eeeee........eeee..eeeee......eeeee.......eee.....eeeeeeee.......hhhhhhhhhh..eee......eee.....ee......ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5gje A    1 APLLLYANRRDLRLVDATNGKENATIVVGGLEDAAAVDFVFSHGLIYWSDVSEEAIKRTEFNKTESVQNVVVSGLLSPDGLACDWLGEKLYWTDSETNRIEVSNLDGSLRKVLFWQELDQPRAIALDPSSGFMYWTDWGEVPKIERAGMDGSSRFIIINSEIYWPNGLTLDYEEQKLYWADAKLNFIHKSNLDGTNRQAVVKGSLPHPFALTLFEDILYWTDWSTHSILACNKYTGEGLREIHSDIFSPMDIHAFSQQRQPNATNPCGIDNGGCSHLCLMSPVKPFYQCACPTGVKLLENGKTCKDGATELLLLARRTDLRRISLDTPDFTDIVLQLEDIRHAIAIDYDPVEGYIYWTDDEVRAIRRSFIDGSGSQFVVTAQIAHPDGIAVDWVARNLYWTDTGTDRIEVTRLNGTMRKILISEDLEEPRAIVLDPMVGYMYWTDWGEIPKIERAALDGSDRVVLVNTSLGWPNGLALDYDEGKIYWGDAKTDKIEVMNTDGTGRRVLVEDKIPHIFGFTLLGDYVYWTDWQRRSIERVHKRSAEREVIIDQLPDLMGLKATNVHRVIGSNPCAEENGGCSHLCLYRPQGLRCACPIGFELISDMKTCIVP  611
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610 


Chain B from PDB  Type:PROTEIN  Length:606
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee..eeeee.......eee........eeeeeee....eeeeee....eeeeee......eeee........eeeee....eeeeee....eeeeee......eeee......eeeeee.....eeeeee.....eeeeee......eeee.....eeeeeee....eeeeee....eeeeee......eeee.....eeeeeee..eeeeee....eeeeee.......eeeee.......eeeehhhhh...hhhhhhhhhh..eeeee...eeeee.....ee......ee....eeeeee...eeee.........ee............eee....eeeeee....eeeee.......eeee.....eeeeeee....eeeeee....eeeeee....eeeeeee.....eeeeee.....eeeeeeee..eeeeeeee......eeee......eeeeeee....eeeeee....eeeeee......eeee......eeeeeee..eeeeee....eeeeee.......eeee.....eeeeeee...hhhhhhh....hhhhhh..eeee.....eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5gje B  631 EAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIRKAQEDGSQGFTVVVSEIQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGVVLKGEQDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKIDMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSCPMHLVLLQDELSC 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    ||1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197      1207      1217      1227      1237      
                                                                                                                                                                                                                                                                                                                                                                                                               1005|                                                                                                                                                                                                                                      
                                                                                                                                                                                                                                                                                                                                                                                                                1013                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:76
                                                                                                             
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...eeeeee..eeeeee............hhhhhhhh..........eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                5gje C  182 KGQEGSVCLRSSDCASGLCCARHFWSKICKPVLKEGQVCTKHRRKGSHGLEIFQRCYCGEGLSCRIQKRLHTCQRH  266
                                   191       201       211       221       231       241       260      
                                                                                             249|       
                                                                                              259
   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 5GJE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GJE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GJE)

(-) Gene Ontology  (117, 126)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5gje)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5gje
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DKK1_HUMAN | O94907
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  LRP6_HUMAN | O75581
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DKK1_HUMAN | O94907
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  LRP6_HUMAN | O75581
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DKK1_HUMAN | O94907: 3s2k 3s8v 3soq 5fww
        LRP6_HUMAN | O75581: 3s2k 3s8v 3s8z 3s94 3sob 3soq 3sov 4a0p 4dg6 4nm5 4nm7 5air 5fww

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5GJE)