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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NECTIN-4 EXTRACELLULAR FRAGMENT D1-D2
 
Authors :  O. J. Harrison, X. Jin, J. Brasch, L. Shapiro
Date :  26 Jun 12  (Deposition) - 22 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D  (2x)
Biol. Unit 4:  E,F  (1x)
Keywords :  Immunoglobulin-Like Domain, Ig Domain, Viral Entry Receptor, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. J. Harrison, J. Vendome, J. Brasch, X. Jin, S. Hong, P. S. Katsamba, G. Ahlsen, R. B. Troyanovsky, S. M. Troyanovsky, B. Honig, L. Shapiro
Nectin Ectodomain Structures Reveal A Canonical Adhesive Interface.
Nat. Struct. Mol. Biol. V. 19 906 2012
PubMed-ID: 22902367  |  Reference-DOI: 10.1038/NSMB.2366

(-) Compounds

Molecule 1 - POLIOVIRUS RECEPTOR-RELATED PROTEIN 4
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293F
    Expression System Common: HUMAN
    Expression System Plasmid: PCEP4
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR DOMAIN (D1-D2, UNP RESIDUES 32-243)
    Gene: PVRL4, LNIR, PRR4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NECTIN-4, IG SUPERFAMILY RECEPTOR LNIR, PROCESSED POLIOVIRUS RECEPTOR-RELATED PROTEIN 4

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (2x): A     
Biological Unit 2 (1x):  BC   
Biological Unit 3 (2x):    D  
Biological Unit 4 (1x):     EF

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 4FRW)

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:52 -A:127
2A:171 -A:223
3B:52 -B:127
4B:171 -B:223
5C:52 -C:127
6C:171 -C:223
7D:52 -D:127
8D:171 -D:223
9E:52 -E:127
10E:171 -E:223
11F:52 -F:127
12F:171 -F:223

(-) Cis Peptide Bonds  (17, 17)

Asymmetric Unit
No.Residues
1Pro A:103 -Pro A:104
2Phe A:132 -Pro A:133
3Ser A:176 -Pro A:177
4Pro B:103 -Pro B:104
5Phe B:132 -Pro B:133
6Ser B:176 -Pro B:177
7Pro C:103 -Pro C:104
8Phe C:132 -Pro C:133
9Ser C:176 -Pro C:177
10Pro D:103 -Pro D:104
11Phe D:132 -Pro D:133
12Ser D:176 -Pro D:177
13Pro E:103 -Pro E:104
14Phe E:132 -Pro E:133
15Ser E:176 -Pro E:177
16Pro F:103 -Pro F:104
17Ser F:176 -Pro F:177

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FRW)

(-) 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:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eeeee....eee..ee......eeeeeeeeee.....eeeeeeee...eeee.hhhh..ee............eee...hhhhheeeeeeeeee..eeeeeeeeeeee.....eeee...ee.....eeeeeeeeee....eeeeee....eeeeeeee....eeeeeeeee..hhhhh..eeeeeee.......eeeeee..ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4frw A  32 GELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLNPGPALEEGQGLTLAASCTAEGSPAPSVTWDTEVKGTTSSRSFKHSRSAAVTSEFHLVPSRSMNGQPLTCVVSHPGLLQDQRITHILHVSHHH 246
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eeeee....eee..ee......eeeeeeeeeee...eeeeeeeee...eeee.......ee............eee...hhhhheeeeeeeeee..eeeeeeeeeeee.....eeee...ee.....eeeeeeeeee....eeeeee....eeeeeeee....eeeeeeeee..hhhhh.eeeeeeee.......eeeeeee.ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4frw B  32 GELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLNPGPALEEGQGLTLAASCTAEGSPAPSVTWDTEVKGTTSSRSFKHSRSAAVTSEFHLVPSRSMNGQPLTCVVSHPGLLQDQRITHILHVSH 244
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   


Chain C from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee...eeeee....eee..ee......eeeeeeeee.......eeeeeee...eeee.hhhh..ee............eee...hhhhheeeeeeeeee..eeeeeeeeeeee.....eeee..........eeeeeeeeee....eeeeee.....eeeeeee....eeeeeeeee.........eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4frw C  32 GELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLNPGPALEEGQGLTLAASCTAEGSPAPSVTWDTEVKGTTSSRSFKHSRSAAVTSEFHLVPSRSMNGQPLTCVVSHPGLLQDQRITHILHV 242
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241 


Chain D from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...eeeee....eee..ee......eeeeeeeee.......eeeeeee...eeee.......ee............eee........eeeeeeeeee..eeeeeeeeeeee.....eeee...ee.....eeeeeeeeee....eeeeee....eeeeeeee....eeeeeeeee..hhhhh..eeeeeee.......eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4frw D  33 ELETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLNPGPALEEGQGLTLAASCTAEGSPAPSVTWDTEVKGTTSSRSFKHSRSAAVTSEFHLVPSRSMNGQPLTCVVSHPGLLQDQRITHILHVSH 244
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242  


Chain E from PDB  Type:PROTEIN  Length:208
                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....ee..............eeeeeee.......eeeeee..............ee.............ee...hhhhheeeeeeee........eeeeeeee.....eeee..........eeeeeeeeee....eeeeee...eeeeeeeee....eeeeeeeee.........eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4frw E  34 LETSDVVTVVLGQDAKLPCFYRGDSGEQVGQVAWARVDAGEGAQELALLHSKYGLHVSPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTFPAGSFQARLRLRVLVPPLPSLNPGPALEEGQGLTLAASCTAEGSPAPSVTWDTEVKGTTSSRSFKHSRSAAVTSEFHLVPSRSMNGQPLTCVVSHPGLLQDQRITHILH 241
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233        


Chain F from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee....eee.....eeee.......eeeee...hhhhh..ee............eee...hhhhheeeeee.....eeeeeee.....eeee..........eeeeeeeeee....ee..............ee....eeeeeeeee..hhhhh.eeeeeeee.......eeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4frw F  36 TSDVVTVVLGQDAKLPCFQVAWARVDAGEGAQELALLHVSPAYEGRVEQPPPPRNPLDGSVLLRNAVQADEGEYECRVSTQARLRLRVLVPPLPSLNPGPALEEGQGLTLAASCTAEGSPAPSVTWDTEVKGTTSSRSFKHSRSAAVTSEFHLVPSRSMNGQPLTCVVSHPGLLQDQRITHILHVSHHH 246
                                    45       |65        75      ||91       101       111       121       131|      147       157       167       177       187       197       207       217       227       237         
                                            53|                82|                                       131|                                                                                                            
                                             64                 89                                        138
   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 4FRW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Phe A:132 - Pro A:133   [ RasMol ]  
    Phe B:132 - Pro B:133   [ RasMol ]  
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  4frw
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 Related Entries

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

UniProtKB/Swiss-Prot
        NECT4_HUMAN | Q96NY8: 4gjt 4jjh

(-) Related Entries Specified in the PDB File

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4fn0 CRYSTAL STRUCTURE OF MURINE NECTIN-2 FRAGMENT D1-D2, 2ND CRYSTAL FORM
4fom CRYSTAL STRUCTURE OF HUMAN NECTIN-3 FULL ECTODOMAIN D1-D3
4fqp CRYSTAL STRUCTURE OF HUMAN NECTIN-LIKE 5 FULL ECTODOMAIN D1-D3
4fs0 CRYSTAL STRUCTURE OF MUTANT F136D OF MOUSE NECTIN-2 FRAGMENT D1-D2