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(-) Description

Title :  STRUCTURE OF THE ECTODOMAIN OF LGR5 IN COMPLEX WITH R-SPONDIN-2 (FU1FU2)
 
Authors :  M. Zebisch, E. Y. Jones
Date :  18 Mar 15  (Deposition) - 08 Jul 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Signaling Protein, Wnt, Lgr, Rspo (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Zebisch, E. Y. Jones
Crystal Structure Of R-Spondin 2 In Complex With The Ectodomains Of Its Receptors Lgr5 And Znrf3.
J. Struct. Biol. V. 191 149 2015
PubMed-ID: 26123262  |  Reference-DOI: 10.1016/J.JSB.2015.05.008

(-) Compounds

Molecule 1 - LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
    ChainsA, C
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293T
    Expression System CommonHUMAN
    Expression System PlasmidPHLSEC
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentECTODOMAIN, RESIDUES 32-487 AND RESIDUES 538-544
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsUNSTRUCTURED LOOP REPLACED WITH SHORT LINKER, A488-H537 TO NGNNGD
    SynonymG-PROTEIN COUPLED RECEPTOR 49, G-PROTEIN COUPLED RECEPTOR 6 7, G-PROTEIN COUPLED RECEPTOR HG38, LGR5
 
Molecule 2 - R-SPONDIN-2
    ChainsB, D
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293T
    Expression System CommonHUMAN
    Expression System PlasmidPHLSEC
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentFU1-FU2, RESIDUES 39-144
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYSTEINE-RICH AND SINGLE THROMBOSPONDIN DOMAIN-CONTAINING PROTEIN 2, CRISTIN-2, MCRISTIN-2, ROOF PLATE-SPECIFIC SPONDIN-2, RSPO2

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER C:58 , ASN C:77BINDING SITE FOR RESIDUE NAG C1001
2AC2SOFTWARETYR A:361 , ARG A:382 , TYR C:361 , ARG C:382BINDING SITE FOR RESIDUE CL A1545
3AC3SOFTWAREHIS A:128 , THR A:131BINDING SITE FOR RESIDUE CL A1546
4AC4SOFTWAREARG B:95BINDING SITE FOR RESIDUE CL B1142
5AC5SOFTWAREARG D:92BINDING SITE FOR RESIDUE CL D1142
6AC6SOFTWARETHR C:131BINDING SITE FOR RESIDUE CL C1545
7AC7SOFTWARELYS A:378 , LYS A:426BINDING SITE FOR RESIDUE CL A1547
8AC8SOFTWARESER A:184 , SER A:186 , ASN A:208BINDING SITE FOR MONO-SACCHARIDE NAG A1001 BOUND TO ASN A 208

(-) SS Bonds  (26, 26)

Asymmetric/Biological Unit
No.Residues
1A:34 -A:40
2A:38 -A:52
3A:348 -A:373
4A:479 -A:541
5A:480 -A:485
6B:40 -B:46
7B:43 -B:52
8B:55 -B:74
9B:78 -B:93
10B:96 -B:104
11B:101 -B:110
12B:113 -B:124
13B:128 -B:141
14C:34 -C:40
15C:38 -C:52
16C:348 -C:373
17C:479 -C:541
18C:480 -C:485
19D:40 -D:46
20D:43 -D:52
21D:55 -D:74
22D:78 -D:93
23D:96 -D:104
24D:101 -D:110
25D:113 -D:124
26D:128 -D:141

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:542 -Pro A:543
2Ser C:542 -Pro C:543

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UFR)

(-) 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:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeee.....eeee................eeeee............hhhhh....eee.....................eee.....................eee.....................eee...........hhhhh.....eee.......ee............eee.......ee............eee.........hhhhhhh....eee.......ee............eee.......ee............eeeee..................eeeee.........hhhhhh....eee...................eee.......ee............eee.......ee............eee..................eee....................eee..hhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ufr A  32 RGCPTHCHCEPDGRMLLRVDCSDLGLSELPSNLSVFTSYLDLSMNNISQLLPNPLPSLRFLEELRLAGNALTYIPKGAFTGLYSLKVLMLQNNQLRHVPTEALQNLRSLQSLRLDANHISYVPPSCFSGLHSLRHLWLDDNALTEIPVQAFRSLSALQAMTLALNKIHHIPDYAFGNLSSLVVLHLHNNRIHSLGKKCFDGLHSLETLDLNYNNLDEFPTAIRTLSNLKELGFHSNNIRSIPEKAFVGNPSLITIHFYDNPIQFVGRSAFQHLPELRTLTLNGASQITEFPDLTGTANLESLTLTGAQISSLPQTVCNQLPNLQVLDLSYNLLEDLPSFSVCQKLQKIDLRHNEIYEIKVDTFQQLLSLRSLNLAWNKIAIIHPNAFSTLPSLIKLDLSSNLLSSFPITGLHGLTHLKLTGNHALQSLISSENFPELKVIEMPYAYQCCAFGVCVQCSP 543
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481   ||    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               485|    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                539    

Chain B from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eeeeee....eeeeee......eeeeee..eeeeee.....eeeeee..eeeee....eee..eee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4ufr B  40 CKGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIENCDSCFSKDFCTKCKVGFYLHRGRCFDECPDGFAPLDETMEC 141
                                    49        59        69        79        89        99       109       119       129       139  

Chain C from PDB  Type:PROTEIN  Length:458
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee...eeeee................eeeee............hhhhh....eee.....................eee.....................eee.....................eee.........hhhhhh......eee.......ee............eee.......ee............eee.........hhhhhhh....eee.......ee............eee.......ee............eeeee..................eeeee.........hhhhhh....eee...................eee.......ee............eee.......ee............eee..................eee....................eee..hhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ufr C  33 GCPTHCHCEPDGRMLLRVDCSDLGLSELPSNLSVFTSYLDLSMNNISQLLPNPLPSLRFLEELRLAGNALTYIPKGAFTGLYSLKVLMLQNNQLRHVPTEALQNLRSLQSLRLDANHISYVPPSCFSGLHSLRHLWLDDNALTEIPVQAFRSLSALQAMTLALNKIHHIPDYAFGNLSSLVVLHLHNNRIHSLGKKCFDGLHSLETLDLNYNNLDEFPTAIRTLSNLKELGFHSNNIRSIPEKAFVGNPSLITIHFYDNPIQFVGRSAFQHLPELRTLTLNGASQITEFPDLTGTANLESLTLTGAQISSLPQTVCNQLPNLQVLDLSYNLLEDLPSFSVCQKLQKIDLRHNEIYEIKVDTFQQLLSLRSLNLAWNKIAIIHPNAFSTLPSLIKLDLSSNLLSSFPITGLHGLTHLKLTGNHALQSLISSENFPELKVIEMPYAYQCCAFGVCVQCSP 543
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482  ||    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              485|    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               539    

Chain D from PDB  Type:PROTEIN  Length:102
                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee........ee....eeeeee....eeeeee......eeee.....eeeee.....eeeeee..eeeee....eee..eee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 4ufr D  40 CKGCLSCSKDNGCSRCQQKLFFFLRREGMRQYGECLHSCPSGYYGHRAPDMNRCARCRIENCDSCFSKDFCTKCKVGFYLHRGRCFDECPDGFAPLDETMEC 141
                                    49        59        69        79        89        99       109       119       129       139  

   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 4UFR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 34)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LGR5_HUMAN | O754734bsr 4bss 4bst 4bsu 4kng 4ufs
        RSPO2_MOUSE | Q8BFU04c99 4ufs

(-) Related Entries Specified in the PDB File

4ufs TERNARY WNT SIGNALLING COMPLEX