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(-) Description

Title :  XENOPUS ZNRF3 ECTODOMAIN CRYSTAL FORM II
 
Authors :  M. Zebisch, E. Y. Jones
Date :  01 Oct 13  (Deposition) - 20 Nov 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.01
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ligase, Wnt, Rnf43, Lgr4, Lgr5, Lgr6, Rspo, R-Spondin, R-Spo, Rspo1, Rspo2, Rspo3, Rspo4, Receptor, Membrane, Signalling (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Zebisch, Y. Xu, C. Krastev, B. T. Macdonald, M. Chen, R. J. C. Gilbert X. He, E. Y. Jones
Structural And Molecular Basis Of Znrf3/Rnf43 Transmembrane Ubiquitin Ligase Inhibition By The Wnt Agonist R-Spondin.
Nat. Commun. V. 4 2787 2013
PubMed-ID: 24225776  |  Reference-DOI: 10.1038/NCOMMS3787

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE ZNRF3
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector: TRANSIENT
    Fragment: ECTODOMAIN, RESIDUES 24-191
    Organism Common: WESTERN CLAWED FROG
    Organism Scientific: XENOPUS (SILURANA) TROPICALIS
    Synonym: ZINC/RING FINGER PROTEIN 3, ZNRF3

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1BR1Ligand/IonBROMIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:110 , THR A:111 , LYS B:163 , ASN B:166BINDING SITE FOR RESIDUE BR A1182

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:80 -A:109
2B:80 -B:109

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C8U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C8U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C8U)

(-) Exons   (0, 0)

(no "Exon" information available for 4C8U)

(-) 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:146
 aligned with ZNRF3_XENTR | Q08D68 from UniProtKB/Swiss-Prot  Length:853

    Alignment length:152
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179  
          ZNRF3_XENTR    30 ETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQLNQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHR 181
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee.....eeeeeeeeeeee........eeeeee..hhhhh.------......eeeeee..hhhhh.....hhhhhhhhhhhh.eeeeeee.....hhhhhhhh..........eeehhhhhhhhhhhhhhh..eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8u A  30 ETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLC------DLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQLNQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHR 181
                                    39        49        59        69        79|      |89        99       109       119       129       139       149       159       169       179  
                                                                             80     87                                                                                              


Chain B from PDB  Type:PROTEIN  Length:144
 aligned with ZNRF3_XENTR | Q08D68 from UniProtKB/Swiss-Prot  Length:853

    Alignment length:152
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179  
          ZNRF3_XENTR    30 ETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQLNQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHR 181
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..ee.....ee.......eee............eeeehhhhh.--------....eeeee...hhhhh.....hhhhhhhhhhhh.eeeee.......hhhhhhh...........ee.hhhhhhhhhhhhh.....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c8u B  30 ETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLC--------YEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQLNQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHR 181
                                    39        49        59        69        79|       89        99       109       119       129       139       149       159       169       179  
                                                                             80       89
   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 4C8U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C8U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C8U)

(-) Gene Ontology  (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ZNRF3_XENTR | Q08D68)
molecular function
    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: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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  4c8u
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 Related Entries

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

UniProtKB/Swiss-Prot
        ZNRF3_XENTR | Q08D68: 4c8t 4c9r 4c9u

(-) Related Entries Specified in the PDB File

4c84 ZEBRAFISH ZNRF3 ECTODOMAIN CRYSTAL FORM I
4c85 ZEBRAFISH ZNRF3 ECTODOMAIN CRYSTAL FORM II
4c86 MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM I
4c8a MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM II
4c8c MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM III
4c8f MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM IV
4c8p MOUSE ZNRF3 ECTODOMAIN CRYSTAL FORM V, DISULFIDE-BRIDGED S90C VARIANT
4c8t XENOPUS ZNRF3 ECTODOMAIN CRYSTAL FORM I
4c8v XENOPUS RSPO2 FU1-FU2 CRYSTAL FORM I
4c8w XENOPUS RSPO2 FU1-FU2 CRYSTAL FORM II
4c99 MOUSE ZNRF3 ECTODOMAIN IN COMPLEX WITH MOUSE RSPO2 FU1 -FU2 CRYSTAL FORM I
4c9a MOUSE ZNRF3 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2 (SELENO MET) CRYSTAL FORM I
4c9e MOUSE ZNRF3 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2 (SELENO MET) CRYSTAL FORM II
4c9r XENOPUS ZNRF3 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2 CRYSTAL FORM I
4c9u XENOPUS ZNRF3 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2 CRYSTAL FORM II
4c9v XENOPUS RNF43 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2