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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN LGR5-RSPO1-RNF43
 
Authors :  P. H. Chen, X. He
Date :  09 May 13  (Deposition) - 19 Jun 13  (Release) - 24 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,E,F,M,P
Keywords :  Leucine-Rich Repeat, Cysteine-Rich Domain, Furin-Repeat, Protease- Associated Domain, Ligand Recognition, Protein-Protein Interaction, N-Linked Glycosylation, Membrane Protein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. H. Chen, X. Chen, Z. Lin, D. Fang, X. He
The Structural Basis Of R-Spondin Recognition By Lgr5 And Rnf43.
Genes Dev. V. 27 1345 2013
PubMed-ID: 23756651  |  Reference-DOI: 10.1101/GAD.219915.113

(-) Compounds

Molecule 1 - LEUCINE-RICH REPEAT-CONTAINING G-PROTEIN COUPLED RECEPTOR 5
    ChainsA, B
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System PlasmidPVLAD6
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentEXTRACELLULAR DOMAIN
    GeneLGR5, GPR49, GPR67
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymG-PROTEIN COUPLED RECEPTOR 49, G-PROTEIN COUPLED RECEPTOR 67, G-PROTEIN COUPLED RECEPTOR HG38
 
Molecule 2 - R-SPONDIN-1
    ChainsM, P
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System PlasmidPVLAD6
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentFURIN REPEATS
    GeneRSPO1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymROOF PLATE-SPECIFIC SPONDIN-1, HRSPO1
 
Molecule 3 - E3 UBIQUITIN-PROTEIN LIGASE RNF43
    ChainsE, F
    EC Number6.3.2.-
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293
    Expression System PlasmidPVLAD6
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentPA DOMAIN
    GeneRNF43
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymRING FINGER PROTEIN 43

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABEFMP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
2NI1Ligand/IonNICKEL (II) ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:183 , SER A:186 , ASN A:208 , HOH A:766BINDING SITE FOR RESIDUE NAG A 601
2AC2SOFTWAREHIS A:199 , HIS A:223 , HIS B:199 , HIS B:223BINDING SITE FOR RESIDUE NI B 601
3AC3SOFTWAREARG B:183 , SER B:184 , SER B:186 , ASN B:208BINDING SITE FOR RESIDUE NAG B 602

(-) SS Bonds  (26, 26)

Asymmetric/Biological Unit
No.Residues
1A:40 -A:34
2A:52 -A:38
3A:373 -A:348
4A:541 -A:479
5B:40 -B:34
6B:52 -B:38
7B:373 -B:348
8B:541 -B:479
9E:119 -E:91
10F:119 -F:91
11M:47 -M:40
12M:53 -M:44
13M:75 -M:56
14M:94 -M:79
15M:105 -M:97
16M:111 -M:102
17M:125 -M:114
18M:142 -M:129
19P:47 -P:40
20P:53 -P:44
21P:75 -P:56
22P:94 -P:79
23P:105 -P:97
24P:111 -P:102
25P:125 -P:114
26P:142 -P:129

(-) Cis Peptide Bonds  (15, 15)

Asymmetric/Biological Unit
No.Residues
1Leu A:60 -Pro A:61
2Leu A:82 -Pro A:83
3Leu A:434 -Ser A:435
4Ser A:542 -Pro A:543
5Asn B:84 -Pro B:85
6Ser B:436 -Phe B:437
7Ser B:542 -Pro B:543
8Asn M:67 -Asp M:68
9Glu M:116 -Gly M:117
10Glu P:116 -Gly P:117
11Asn E:179 -Gln E:180
12Lys F:54 -Met F:55
13Ser F:135 -Ala F:136
14Lys F:178 -Asn F:179
15Lys F:181 -Ala F:182

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KNG)

(-) 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:461
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee...eeeee................eeeee.....................eee.....................eee.....................eee.....................eee.........hhhhhh......eee.......ee............eee.......ee............eee.........hhhhhhh....eee.......ee............eee.......ee.............eeee..................eeeee.........hhhhhh....eee...................eee.......ee............eee.......ee............eee..................eee....................eee.................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kng A  30 GPRGCPTHCHCEPDGRMLLRVDCSDLGLSELPSNLSVFTSYLDLSMNNISQLLPNPLPSLRFLEELRLAGNALTYIPKGAFTGLYSLKVLMLQNNQLRHVPTEALQNLRSLQSLRLDANHISYVPPSCFSGLHSLRHLWLDDNALTEIPVQAFRSLSALQAMTLALNKIHHIPDYAFGNLSSLVVLHLHNNRIHSLGKKCFDGLHSLETLDLNYNNLDEFPTAIRTLSNLKELGFHSNNIRSIPEKAFVGNPSLITIHFYDNPIQFVGRSAFQHLPELRTLTLNGASQITEFPDLTGTANLESLTLTGAQISSLPQTVCNQLPNLQVLDLSYNLLEDLPSFSVCQKLQKIDLRHNEIYEIKVDTFQQLLSLRSLNLAWNKIAIIHPNAFSTLPSLIKLDLSSNLLSSFPITGLHGLTHLKLTGNHALQSLISSENFPELKVIEMPYAYQCCAFGHSVQCSP 543
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479   ||  542 
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               483|      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                537      

Chain B from PDB  Type:PROTEIN  Length:463
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee...eeeee................eeeee.....................eee.....................eee.....................eee.....................eee.........hhhhhh......eee.......ee............eee.......ee............eee.........hhhhhhh....eee.......ee............eee.......ee.............eeee..................eeeee.........hhhhhh....eee...................eee.......ee............eee.......ee............eee..................eee....................eee...hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kng B  30 GPRGCPTHCHCEPDGRMLLRVDCSDLGLSELPSNLSVFTSYLDLSMNNISQLLPNPLPSLRFLEELRLAGNALTYIPKGAFTGLYSLKVLMLQNNQLRHVPTEALQNLRSLQSLRLDANHISYVPPSCFSGLHSLRHLWLDDNALTEIPVQAFRSLSALQAMTLALNKIHHIPDYAFGNLSSLVVLHLHNNRIHSLGKKCFDGLHSLETLDLNYNNLDEFPTAIRTLSNLKELGFHSNNIRSIPEKAFVGNPSLITIHFYDNPIQFVGRSAFQHLPELRTLTLNGASQITEFPDLTGTANLESLTLTGAQISSLPQTVCNQLPNLQVLDLSYNLLEDLPSFSVCQKLQKIDLRHNEIYEIKVDTFQQLLSLRSLNLAWNKIAIIHPNAFSTLPSLIKLDLSSNLLSSFPITGLHGLTHLKLTGNHALQSLISSENFPELKVIEMPYAYQCCAFHSVQCSPSPG 546
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479  ||   543   
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              482|         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               537         

Chain E from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..........eeeeeee........eeeeeee...................eeeee............hhhhhhhhhhhh...eeeee.hhhhhhhhhh.........eeeehhhhhhhhhhhhh......eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kng E  44 QKAIIRVIPLKMDPTGKLNLTLEGVFAGVAEITPAEGKLMQSHPLYLCNASDDDNLEPGFISIVKLESPRRAPRPCLSLASKARMAGERGASAVLFDITEDRAAAEQLQQPLGLTWPVVLIWGNDAEKLMEFVYKNQKAHVRIELKEPP 192
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183         

Chain F from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..........eeeeeee........eeeeeee...................eeeee............hhhhhhhhhhhhh...eeee.hhhhhhhhhh.........eeeehhhhhhhhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kng F  44 QKAIIRVIPLKMDPTGKLNLTLEGVFAGVAEITPAEGKLMQSHPLYLCNASDDDNLEPGFISIVKLESPRRAPRPCLSLASKARMAGERGASAVLFDITEDRAAAEQLQQPLGLTWPVVLIWGNDAEKLMEFVYKNQKAHVRIELKEP 191
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183        

Chain M from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee........ee....eeeeee....eeeeee......eeee......eeee.....eeeeee..eeeee....eee..eee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4kng M  40 CAKGCELCSEVNGCLKCSPKLFILLERNDIRQVGVCLPSCPPGYFDARNPDMNKCIKCKIEHCEACFSHNFCTKCKEGLYLHKGRCYPACPEGTMECS 143
                                    49        59        69        79        89        99       109       119       129  ||    
                                                                                                                      132|    
                                                                                                                       139    

Chain P from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee........ee....eeeeee....eeeeee......eeee......eeee.....eeeeee..eeeee....eee..eee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 4kng P  40 CAKGCELCSEVNGCLKCSPKLFILLERNDIRQVGVCLPSCPPGYFDARNPDMNKCIKCKIEHCEACFSHNFCTKCKEGLYLHKGRCYPACPEGC 142
                                    49        59        69        79        89        99       109       119       129  ||
                                                                                                                      132|
                                                                                                                       142

   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 4KNG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 51)

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 4ufr 4ufs
        RSPO1_HUMAN | Q2MKA74bso 4bsp 4bsr 4bss 4bst 4bsu 4cdk 4kt1 4li2 4qxf

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4KNG)