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(-) Description

Title :  XENOPUS ZNRF3 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2 CRYSTAL FORM II
 
Authors :  M. Zebisch, E. Y. Jones
Date :  03 Oct 13  (Deposition) - 20 Nov 13  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Ligase-Signaling Protein Complex, Wnt, Rnf43, Lgr4, Lgr5, Lgr6, Rspo, R-Spondin, R-Spo, Rspo1, 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, C
    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
    Organism Taxid: 8364
    Synonym: ZINC/RING FINGER PROTEIN 3, ZNRF3
 
Molecule 2 - R-SPONDIN-2
    Chains: B, D
    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: FU1-FU2, RESIDUES 35-144
    Organism Common: WESTERN CLAWED FROG
    Organism Scientific: XENOPUS (SILURANA) TROPICALIS
    Organism Taxid: 8364
    Synonym: ROOF PLATE-SPECIFIC SPONDIN-2, RSPO2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): AB  
Biological Unit 2 (2x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4C9U)

(-) Sites  (0, 0)

(no "Site" information available for 4C9U)

(-) SS Bonds  (17, 17)

Asymmetric Unit
No.Residues
1A:80 -A:109
2B:40 -B:46
3B:43 -B:52
4B:55 -B:74
5B:78 -B:93
6B:96 -B:104
7B:101 -B:110
8B:113 -B:124
9B:128 -B:141
10C:80 -C:109
11D:40 -D:46
12D:43 -D:52
13D:55 -D:74
14D:78 -D:93
15D:96 -D:104
16D:101 -D:110
17D:113 -D:124

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C9U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C9U)

(-) Exons   (0, 0)

(no "Exon" information available for 4C9U)

(-) 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:161
 aligned with ZNRF3_XENTR | Q08D68 from UniProtKB/Swiss-Prot  Length:853

    Alignment length:161
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 
          ZNRF3_XENTR    22 APGESLAKETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQLNQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHRP 182
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee.....eeeeeeeeeeee........eeeeeee...................eeeeee............hhhhhhhhhhhh.eeeeeee....hhhhhhhh..........eeeehhhhhhhhhhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c9u A  22 ETGESLAKETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQLNQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHRP 182
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 


Chain B from PDB  Type:PROTEIN  Length:103
 aligned with RSPO2_XENTR | Q5M7L6 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:103
                                    48        58        68        78        88        98       108       118       128       138   
          RSPO2_XENTR    39 ICKGCLSCSKDNGCLRCQPKLFFYLRREGMRQYGECLQSCPPGYYGVRGPDMNRCSRCRIENCDSCFSRDFCIKCKSGFYSHKGQCFEECPEGFAPLDDTMVC 141
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeee....eeeeeee..eeeeeee......eeeee....eeeee.....eeeeee..eeeee....eee..eee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 4c9u B  39 ICKGCLSCSKDNGCLRCQPKLFFYLRREGMRQYGECLQSCPPGYYGVRGPDMNRCSRCRIENCDSCFSRDFCIKCKSGFYSHKGQCFEECPEGFAPLDDTMVC 141
                                    48        58        68        78        88        98       108       118       128       138   


Chain C from PDB  Type:PROTEIN  Length:155
 aligned with ZNRF3_XENTR | Q08D68 from UniProtKB/Swiss-Prot  Length:853

    Alignment length:155
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177     
          ZNRF3_XENTR    28 AKETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQLNQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHRP 182
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee.....eeeeeeeeeeee........eeeeeee...................eeeeee............hhhhhhhhhhhh.eeeeeee....hhhhhhhh..........eeeehhhhhhhhhhhhhhh..eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c9u C  28 AKETAFVEVVLFESSPNGDYKTHTTELQGRFSRAGATISAEGEIVQMHPLGLCNNNDEEDLYEYGWVGVVKLEQPEMDPKPCLTVLGKAKRAVQRGATAVIFDVSDNPDAVEQLNQGLEDPLKRPVVYMKGMDAIKLMNIVNKQKGARARIQHRP 182
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177     


Chain D from PDB  Type:PROTEIN  Length:86
 aligned with RSPO2_XENTR | Q5M7L6 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:86
                                    48        58        68        78        88        98       108       118      
          RSPO2_XENTR    39 ICKGCLSCSKDNGCLRCQPKLFFYLRREGMRQYGECLQSCPPGYYGVRGPDMNRCSRCRIENCDSCFSRDFCIKCKSGFYSHKGQC 124
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee...eeeee....eeeeeee..eeeeeee......eeeee....eeeee.....eeee.....eeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 4c9u D  39 ICKGCLSCSKDNGCLRCQPKLFFYLRREGMRQYGECLQSCPPGYYGVRGPDMNRCSRCRIENCDSCFSRDFCIKCKSGFYSHKGQC 124
                                    48        58        68        78        88        98       108       118
   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 4C9U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C9U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C9U)

(-) Gene Ontology  (18, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (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.

Chain B,D   (RSPO2_XENTR | Q5M7L6)
molecular function
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
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:0050896    response to stimulus    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 stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RSPO2_XENTR | Q5M7L6: 4c8v 4c8w 4c9a 4c9e 4c9r 4c9v
        ZNRF3_XENTR | Q08D68: 4c8t 4c8u 4c9r

(-) 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
4c8u XENOPUS ZNRF3 ECTODOMAIN CRYSTAL FORM II
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
4c9v XENOPUS RNF43 ECTODOMAIN IN COMPLEX WITH XENOPUS RSPO2 FU1-FU2