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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NECTIN-1 FULL ECTODOMAIN (D1-D3)
 
Authors :  O. J. Harrison, J. Brasch, L. Shapiro
Date :  16 Jun 12  (Deposition) - 22 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (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 1
    Chains: A, B, C, D
    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-D3, UNP RESIDUES 31-337)
    Gene: PVRL1, HVEC, PRR1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NECTIN-1, HERPES VIRUS ENTRY MEDIATOR C, HERPESVIRUS ENTRY MEDIATOR C, HVEC, HERPESVIRUS IG-LIKE RECEPTOR, HIGR

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1FMT4Ligand/IonFORMIC ACID
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:116 , ASN A:176 , ASN A:202 , THR A:204 , NAG A:402BINDING SITE FOR RESIDUE NAG A 401
02AC2SOFTWARENAG A:401BINDING SITE FOR RESIDUE NAG A 402
03AC3SOFTWAREVAL A:183BINDING SITE FOR RESIDUE FMT A 403
04AC4SOFTWAREILE B:43 , LEU B:116 , ASN B:176 , ASN B:202 , THR B:204 , NAG B:402BINDING SITE FOR RESIDUE NAG B 401
05AC5SOFTWARENAG B:401BINDING SITE FOR RESIDUE NAG B 402
06AC6SOFTWAREVAL B:183 , HIS B:231BINDING SITE FOR RESIDUE FMT B 403
07AC7SOFTWARELEU C:116 , ASN C:176 , ASN C:202 , THR C:204 , NAG C:402BINDING SITE FOR RESIDUE NAG C 401
08AC8SOFTWAREASN C:176 , NAG C:401BINDING SITE FOR RESIDUE NAG C 402
09AC9SOFTWAREVAL C:182 , VAL C:183 , HIS C:231BINDING SITE FOR RESIDUE FMT C 403
10BC1SOFTWAREASN D:176 , ASN D:200 , ASN D:202 , THR D:204 , NAG D:402BINDING SITE FOR RESIDUE NAG D 401
11BC2SOFTWAREASN D:176 , ASN D:200 , NAG D:401BINDING SITE FOR RESIDUE NAG D 402
12BC3SOFTWAREVAL D:183 , HIS D:231BINDING SITE FOR RESIDUE FMT D 403

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:51 -A:124
2A:172 -A:226
3A:269 -A:316
4B:51 -B:124
5B:172 -B:226
6B:269 -B:316
7C:51 -C:124
8C:172 -C:226
9C:269 -C:316
10D:51 -D:124
11D:172 -D:226
12D:269 -D:316

(-) Cis Peptide Bonds  (21, 21)

Asymmetric Unit
No.Residues
1Ala A:91 -Pro A:92
2Pro A:92 -Tyr A:93
3Phe A:129 -Pro A:130
4Lys A:178 -Pro A:179
5Asn A:274 -Pro A:275
6Lys A:291 -Gly A:292
7Ala B:91 -Pro B:92
8Phe B:129 -Pro B:130
9Lys B:178 -Pro B:179
10Asn B:274 -Pro B:275
11Lys B:291 -Gly B:292
12Ala C:91 -Pro C:92
13Phe C:129 -Pro C:130
14Lys C:178 -Pro C:179
15Asn C:274 -Pro C:275
16Lys C:291 -Gly C:292
17Ala D:91 -Pro D:92
18Phe D:129 -Pro D:130
19Lys D:178 -Pro D:179
20Asn D:274 -Pro D:275
21Lys D:291 -Gly D:292

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FMF)

(-) 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:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eee...........eeeeeeeeee.....eeeeeee...eeee.......eee.........eee...hhhhheeeeeeeeee..eeeeeeeeeeee...eeeeee....ee........eeeeeeeeeee....eeeee.....eeeeeeee.....eeeeeeeee..hhhhh....eeeeee..eeeee.....eeeeeeeeee............eeeeeeeeee....eeeeee........eeee..eeee.........eeeeeeeee..eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmf A  36 NDSMYGFIGTDVVLHCSFANPLPSVKITQVTWQKSTNGSKQNVAIYNPSMGVSVLAPYRERVEFLRPSFTDGTIRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKKGQDDKVLVATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQQSLACIVNYHMDRFKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFKGPINYSLAGTYICEATNPIGTRSGQVEVNITEFP 337
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335  


Chain B from PDB  Type:PROTEIN  Length:299
                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eee...........eeeeeeeeeee..eeeeeeeee...eeee.......eee.........eee...hhhhheeeeeeeeee..eeeeeeeeeeee...eeeeee....ee........eeeeeeeeeee....eeeeee....eeeeeeee.....eeeeeeeee..hhhhh..eeeeeeee..eeeeeeee..eeeeeeeeee............eeeeeeeeee....eeeeee........eeee..eeee.........eeeeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmf B  36 NDSMYGFIGTDVVLHCSFANPLPSVKITQVTWQKSTNGSKQNVAIYNPSMGVSVLAPYRERVEFLRPSFTDGTIRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKKGQDDKVLVATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQQSLACIVNYHMDRFKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFKGPINYSLAGTYICEATNPIGTRSGQVEVNIT 334
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325         


Chain C from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eee...........eeeeeeeeee....eeeeeeee...eeee.......eee.........eee...hhhhheeeeeeeeee..eeeeeeeeeeee...eeeeee....ee........eeeeeeeeeee....eeeeee....eeeeeeee.....eeeeeeeee..hhhhh..eeeeeeee..eeeeeeee..eeeeeeeeee............eeeeeeeeee....eeeeee........eeee..eeee.........eeeeeeeee..eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmf C  36 NDSMYGFIGTDVVLHCSFANPLPSVKITQVTWQKSTNGSKQNVAIYNPSMGVSVLAPYRERVEFLRPSFTDGTIRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKKGQDDKVLVATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQQSLACIVNYHMDRFKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFKGPINYSLAGTYICEATNPIGTRSGQVEVNITEF 336
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335 


Chain D from PDB  Type:PROTEIN  Length:302
                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee....eee...........eeeeeeeeee.....eeeeeee...eeee.......eee.........eee...hhhhheeeeeeeeee..eeeeeeeeeeee...eeeeee....ee........eeeeeeeeeee....eeeeee....eeeeeeee.....eeeeeeeee..hhhhh..eeeeeeee..eeeeeeee..eeeeeeeeee............eeeeeeeeee....eeeeee........eeee..eeee.........eeeeeeeee..eeeeeeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmf D  36 NDSMYGFIGTDVVLHCSFANPLPSVKITQVTWQKSTNGSKQNVAIYNPSMGVSVLAPYRERVEFLRPSFTDGTIRLSRLELEDEGVYICEFATFPTGNRESQLNLTVMAKPTNWIEGTQAVLRAKKGQDDKVLVATCTSANGKPPSVVSWETRLKGEAEYQEIRNPNGTVTVISRYRLVPSREAHQQSLACIVNYHMDRFKESLTLNVQYEPEVTIEGFDGNWYLQRMDVKLTCKADANPPATEYHWTTLNGSLPKGVEAQNRTLFFKGPINYSLAGTYICEATNPIGTRSGQVEVNITEFP 337
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
   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 4FMF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (43, 43)

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  Cis Peptide Bonds
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    Ala C:91 - Pro C:92   [ RasMol ]  
    Ala D:91 - Pro D:92   [ RasMol ]  
    Asn A:274 - Pro A:275   [ RasMol ]  
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        NECT1_HUMAN | Q15223: 3alp 3sku 3u82 3u83 4myw

(-) Related Entries Specified in the PDB File

4fmk CRYSTAL STRUCTURE OF NECTIN-2
4fn0 CRYSTAL STRUCTURE OF NECTIN-2, 2ND CRYSTAL FORM