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(-) Description

Title :  STRUCTURE OF ZNRF3 ECTODOMAIN
 
Authors :  W. C. Peng, W. De Lau, P. K. Madoori, F. Forneris, J. C. M. Granneman, H. C P. Gros
Date :  01 Nov 13  (Deposition) - 08 Jan 14  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ligase, Wnt Signaling, Adult Stem Cells, E3 Ligase, Protease- Associated Domain, Zinc Ring Finger, Lgr5, R-Spondin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. C. Peng, W. De Lau, P. K. Madoori, F. Forneris, J. C. M. Granneman, H. Clevers, P. Gros
Structures Of Wnt-Antagonist Znrf3 And Its Complex With R- Spondin 1 And Implications For Signaling.
Plos One V. 8 83110 2013
PubMed-ID: 24349440  |  Reference-DOI: 10.1371/JOURNAL.PONE.0083110

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
    ChainsA, B
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK 293
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentECTODOMAIN, RESIDUES 53-205
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymZINC/RING FINGER PROTEIN 3

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2FMT1Ligand/IonFORMIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2FMT1Ligand/IonFORMIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2FMT-1Ligand/IonFORMIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:93 , ALA A:94 , GLU A:95 , ILE A:205 , HOH A:2050 , HOH A:2052 , SER B:93 , ALA B:94 , GLU B:95 , ILE B:205BINDING SITE FOR RESIDUE EDO A1209
2AC2SOFTWARELEU A:137 , THR A:138 , GLY A:141 , HOH A:2115 , HOH A:2169BINDING SITE FOR RESIDUE FMT A1210
3AC3SOFTWARELYS A:125 , ASP A:157 , SER A:159BINDING SITE FOR RESIDUE EDO A1211
4AC4SOFTWAREILE A:189 , ASN A:193 , HOH A:2170BINDING SITE FOR RESIDUE EDO A1212
5AC5SOFTWARELYS B:125 , ASP B:157 , SER B:159 , HOH B:2098BINDING SITE FOR RESIDUE EDO B1208
6AC6SOFTWARECYS B:136 , LEU B:137BINDING SITE FOR RESIDUE EDO B1209

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:107 -A:136
2B:107 -B:136

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn A:110 -Asp A:111
2Asn B:109 -Asn B:110
3Asp B:111 -Glu B:112
4Glu B:112 -Glu B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CDJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4CDJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4CDJ)

(-) 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:153
 aligned with ZNRF3_MOUSE | Q5SSZ7 from UniProtKB/Swiss-Prot  Length:913

    Alignment length:153
                                    62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   
          ZNRF3_MOUSE    53 KETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHL 205
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeee.......eeeeeeeeeee........eeeeeee.hhhhhh............eeeeee..hhhhh.....hhhhhhhhhhhh.eeeeeee.....hhhhhhh..........eeeehhhhhhhhhhhhh....eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cdj A  56 KETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQHL 208
                                    65        75        85        95       105       115       125       135       145       155       165       175       185       195       205   

Chain B from PDB  Type:PROTEIN  Length:154
 aligned with ZNRF3_MOUSE | Q5SSZ7 from UniProtKB/Swiss-Prot  Length:913

    Alignment length:157
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       
          ZNRF3_MOUSE    48 GAARAKETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQH 204
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .---...eeeeeeeeeee.....eeeeeeeeeeee........eeeeeee.hhhhhh............eeeeee..hhhhh.....hhhhhhhhhhhh.eeeeeee.....hhhhhhh..........eeeehhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cdj B  54 G---SKETAFVEVVLFESSPSGDYTTHTTGLTGRFSRAGAMLSAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPELDPKPCLTVLGKAKRAVQRGATAVIFDVSENPEAIDQLNQGSEDPLKRPVVYVKGADAIKLMNIVNKQKVARARIQH 207
                            |   |   60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       
                           54  55                                                                                                                                                        

   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 4CDJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CDJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CDJ)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ZNRF3_MOUSE | Q5SSZ7)
molecular function
    GO:0005109    frizzled binding    Interacting selectively and non-covalently with the frizzled (fz) receptor.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0038018    Wnt receptor catabolic process    The chemical reactions and pathways resulting in the breakdown of a Wnt receptor. Internalized Wnt receptors can be recycled to the plasma membrane or sorted to lysosomes for protein degradation.
    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:0060071    Wnt signaling pathway, planar cell polarity pathway    The series of molecular signals initiated by binding of a Wnt protein to a receptor on the surface of the target cell where activated receptors signal via downstream effectors including C-Jun N-terminal kinase (JNK) to modulate cytoskeletal elements and control cell polarity.
    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: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: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:2000051    negative regulation of non-canonical Wnt signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of non-canonical Wnt signaling pathway.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0072089    stem cell proliferation    The multiplication or reproduction of stem cells, resulting in the expansion of a stem cell population. A stem cell is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into specialized cells.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    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:0005887    integral component of plasma membrane    The component of the plasma 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: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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 Related Entries

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

UniProtKB/Swiss-Prot
        ZNRF3_MOUSE | Q5SSZ74c86 4c8a 4c8c 4c8f 4c8p 4c99 4c9a 4c9e 4cdk 4ufs

(-) Related Entries Specified in the PDB File

4cdk STRUCTURE OF ZNRF3-RSPO1