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(-) Description

Title :  WNT MODULATOR KREMEN IN COMPLEX WITH DKK1 (CRD2) AND LRP6 (PE3PE4)
 
Authors :  M. Zebisch, V. A. Jackson, E. Y. Jones
Date :  21 Feb 16  (Deposition) - 20 Jul 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (1x)
Keywords :  Signaling Protein, Wnt, Cell Surface, Signalling, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Zebisch, V. A. Jackson, Y. Zhao, E. Y. Jones
Structure Of The Dual-Mode Wnt Regulator Kremen1 And Insight Into Ternary Complex Formation With Lrp6 And Dickkopf
Structure V. 24 1599 2016
PubMed-ID: 27524201  |  Reference-DOI: 10.1016/J.STR.2016.06.020

(-) Compounds

Molecule 1 - LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System CommonHUMAN
    Expression System PlasmidPHLSEC
    Expression System Taxid9606
    Expression System VectorPHLSEC
    FragmentPE3PE4, RESIDUES 630-1246
    GeneLRP6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLRP-6
 
Molecule 2 - KREMEN PROTEIN 1
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System CommonHUMAN
    Expression System PlasmidPHLSEC
    Expression System Taxid9606
    Expression System VectorPHLSEC
    FragmentECD, RESIDUES 30-322
    GeneKREMEN1, KREMEN, KRM1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDICKKOPF RECEPTOR, KRINGLE DOMAIN-CONTAINING TRANSMEMBRANE PROTEIN 1, KRINGLE-CONTAINING PROTEIN MARKING THE EYE AND THE NOSE
 
Molecule 3 - DICKKOPF-RELATED PROTEIN 1
    ChainsC
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System CommonHUMAN
    Expression System PlasmidPHLSEC
    Expression System Taxid9606
    FragmentCRD2, RESIDUES 182-266
    GeneDKK1, UNQ492/PRO1008
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHDKK-1, SK

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:266 , SER B:305 , ASP B:306 , ASN B:309BINDING SITE FOR RESIDUE CA B1323

(-) SS Bonds  (19, 19)

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:32 -B:114
8B:55 -B:95
9B:84 -B:109
10B:122 -B:186
11B:147 -B:167
12B:151 -B:169
13B:190 -B:198
14B:214 -B:240
15C:189 -C:201
16C:195 -C:210
17C:200 -C:237
18C:220 -C:245
19C:239 -C:263

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn B:128 -Pro B:129
2Phe B:230 -Pro B:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FWW)

(-) 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:612
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               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......eeeeeee....eeeeee.....eeeeee......eeee.....eeeeeee....eeeeee....eeeeee......eeee.....eeeeeee..eeeeee....eeeeee.......eeeee.......eeee........hhhhhhhhhh..eeee.....eeee.....ee......ee....eeeee....eeee.........ee........eeeeeee....eeeeee....eeeee.......eeee.....eeeeeee....eeeeee....eeeeee....eeeeeee.....eeeeeee....eeeeeee....eeeeee.......eeee......eeeeeee....eeeeee....eeeeee......eeee......eeeeeee..eeeeee....eeeeee.......eeeee......eeeee...hhhhhhh....hhhhhh....................ee......ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5fww A  628 ADPEAFLLFSRRADIRRISLETNNNNVAIPLTGVKEASALDFDVTDNRIYWTDISLKTISRAFMNGSALEHVVEFGLDYPEGMAVDWLGKNLYWADTGTNRIEVSKLDGQHRQVLVWKDLDSPRALALDPAEGFMYWTEWGGKPKIDRAAMDGSERTTLVPNVGRANGLTIDYAKRRLYWTDLDTNLIESSNMLGLNREVIADDLPHPFGLTQYQDYIYWTDWSRRSIERANKTSGQNRTIIQGHLDYVMDILVFHSSRQSGWNECASSNGHCSHLCLAVPVGGFVCGCPAHYSLNADNRTCSAPTTFLLFSQKSAINRMVIDEQQSPDIILPIHSLRNVRAIDYDPLDKQLYWIDSRQNMIRKAQEDGSQGFTVVVSEIQPYDLSIDIYSRYIYWTCEATNVINVTRLDGRSVGVVLKGEQDRPRAIVVNPEKGYMYFTNLQERSPKIERAALDGTEREVLFFSGLSKPIALALDSRLGKLFWADSDLRRIESSDLSGANRIVLEDSNILQPVGLTVFENWLYWIDKQQQMIEKIDMTGREGRTKVQARIAQLSDIHAVKELNLQEYRQHPCAQDNGGCSHICLVKGDGTTRCSCPMHLVLLQDELSCGEP 1246
                                   637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154      1164      1174      1184      1194      1204      1214      1224      1234      1244  
                                                                                                                                                                                                                                                                                                                                                                                                                  1005|                                                                                                                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                                                                   1013                                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:288
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........................hhhhh............hhhhh...............eee....eee..........eeeeee..........eeee....hhhhhhhhhhhh...eeeee...eeeee...........hhhhh................eeeeee.......eee...eeeee............eeeeeee.....eeeeeeeeee......eeeeee.....eeeeee.......eeee...eeeeeee........eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5fww B   30 PECFTANGADYRGTQNWTALQGGKPCLFWNETFQHPYNTLKYPNGEGGLGEHNYCRNPDGDVSPWCYVGVYWKYCEIPACQMPGNLGCYKDHGNPPPLTGTSKTSNKLTIQTCISFCRSQRFKFAGMESGYACFCGNNPDYWKYGEAASTECNSVCFGDHTQPCGGDGRIILFDTLVGACGGNYSAMSSVVYSPDFPDTYATGRVCYWTIRVPGASHIHFSFPLFDIRDSADMVELLDGYTHRVLARFHGRSRPPLSFNVSLDFVILYFFSDRINQAQGFAVLYQAVK  322
                                    39        49        59        69        79        89       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314        
                                                                                              97|                                                                                                                                                                                                                           
                                                                                              103                                                                                                                                                                                                                           

Chain C from PDB  Type:PROTEIN  Length:76
                                                                                                             
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................eeeeee..eeeeee......ee.....hhhhhhh...........eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                5fww 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 5FWW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (119, 132)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DKK1_HUMAN | O949073s2k 3s8v 3soq 5gje
        KREM1_HUMAN | Q96MU85fws 5fwt 5fwu 5fwv
        LRP6_HUMAN | O755813s2k 3s8v 3s8z 3s94 3sob 3soq 3sov 4a0p 4dg6 4nm5 4nm7 5air 5gje

(-) Related Entries Specified in the PDB File

5fws STRUCTURE OF A WNT REGULATOR
5fwt STRUCTURE OF A WNT REGULATOR
5fwu STRUCTURE OF A WNT REGULATOR
5fwv STRUCTURE OF A WNT REGULATOR