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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN NECTIN-3 FULL ECTODOMAIN (D1-D3)
 
Authors :  O. J. Harrison, X. Jin, J. Brasch, L. Shapiro
Date :  20 Jun 12  (Deposition) - 22 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.93
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Immunoglobulin-Like Domain, Ig Domain, 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 3
    Chains: A
    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: ECTODOMAIN (D1-D3, UNP RESIDUES 58-359)
    Gene: PVRL3, PRR3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NECTIN-3, CDW113

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2FUC1Ligand/IonALPHA-L-FUCOSE
3MAN6Ligand/IonALPHA-D-MANNOSE
4NAG9Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 40)
No.NameCountTypeFull Name
1BMA8Ligand/IonBETA-D-MANNOSE
2FUC2Ligand/IonALPHA-L-FUCOSE
3MAN12Ligand/IonALPHA-D-MANNOSE
4NAG18Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:73 , HIS A:136 , NAG A:402BINDING SITE FOR RESIDUE NAG A 401
02AC2SOFTWARENAG A:401 , BMA A:403BINDING SITE FOR RESIDUE NAG A 402
03AC3SOFTWARENAG A:402 , MAN A:404 , MAN A:405BINDING SITE FOR RESIDUE BMA A 403
04AC4SOFTWAREBMA A:403BINDING SITE FOR RESIDUE MAN A 404
05AC5SOFTWAREBMA A:403BINDING SITE FOR RESIDUE MAN A 405
06AC6SOFTWAREASN A:125 , ASP A:130 , NAG A:407BINDING SITE FOR RESIDUE NAG A 406
07AC7SOFTWARENAG A:406 , BMA A:408BINDING SITE FOR RESIDUE NAG A 407
08AC8SOFTWARENAG A:407BINDING SITE FOR RESIDUE BMA A 408
09AC9SOFTWAREASN A:186 , ASP A:277 , NAG A:410 , FUC A:411BINDING SITE FOR RESIDUE NAG A 409
10BC1SOFTWARENAG A:409 , FUC A:411 , BMA A:412BINDING SITE FOR RESIDUE NAG A 410
11BC2SOFTWAREGLU A:187 , VAL A:189 , NAG A:409 , NAG A:410BINDING SITE FOR RESIDUE FUC A 411
12BC3SOFTWARENAG A:410 , MAN A:413 , MAN A:414BINDING SITE FOR RESIDUE BMA A 412
13BC4SOFTWAREBMA A:412BINDING SITE FOR RESIDUE MAN A 413
14BC5SOFTWAREBMA A:412BINDING SITE FOR RESIDUE MAN A 414
15BC6SOFTWAREPHE A:140 , PHE A:220 , ASN A:222 , NAG A:416BINDING SITE FOR RESIDUE NAG A 415
16BC7SOFTWARETHR A:197 , NAG A:415 , BMA A:417BINDING SITE FOR RESIDUE NAG A 416
17BC8SOFTWARENAG A:416 , MAN A:418 , MAN A:419BINDING SITE FOR RESIDUE BMA A 417
18BC9SOFTWAREBMA A:417BINDING SITE FOR RESIDUE MAN A 418
19CC1SOFTWAREBMA A:417BINDING SITE FOR RESIDUE MAN A 419
20CC2SOFTWAREGLN A:310 , ASN A:331BINDING SITE FOR RESIDUE NAG A 420

(-) SS Bonds  (3, 3)

Asymmetric Unit
No.Residues
1A:78 -A:148
2A:193 -A:246
3A:291 -A:338

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:115 -Glu A:116
2Phe A:153 -Pro A:154
3Lys A:199 -Pro A:200
4Asn A:296 -Pro A:297

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FOM)

(-) 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 .........eee....eee.........eeeeeeeee....eeeeeee.....eee.......eee.........eee...hhhhheeeeeeeee...eeeeeeeeeeee...eeeeee...........eeeeeeeeeee....eeee........eeeee.....eeeeeeeee..hhhhh..eeeeeee.......eeeeee....eeeee........ee......eee..eeee..eeeeeeee..............eee...........eeeeeeee..eeeeeeee..ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fom A  58 GPIIVEPHVTAVWGKNVSLKCLIEVNETITQISWEKIHGKSSQTVAVHHPQYGFSVQGEYQGRVLFKNYSLNDATITLHNIGFSDSGKYICKAVTFPLGNAQSSTTVTVLVEPTVSLIKGPDSLIDGGNETVAAICIAATGKPVAHIDWEGDLGEMESTTTSFPNETATIISQYKLFPTRFARGRRITCVVKHPALEKDIRYSFILDIQYAPEVSVTGYDGNWFVGRKGVNLKCNADANPPPFKSVWSRLDGQWPDGLLASDNTLHFVHPLTFNYSGVYICKVTNSLGQRSDQKVIYISDPP 359
                                    67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357
   Legend:   → Mismatch (orange background)
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  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 4FOM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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(-) Related Entries Specified in the PDB File

4fmf CRYSTAL STRUCTURE OF HUMAN NECTIN-1 FULL ECTODOMAIN D1-D3
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4fn0 CRYSTAL STRUCTURE OF MURINE NECTIN-2 FRAGMENT D1-D2, 2ND CRYSTAL FORM
4fqp CRYSTAL STRUCTURE OF HUMAN NECTIN-LIKE 5 FULL ECTODOMAIN D1-D3
4frw CRYSTAL STRUCTURE OF HUMAN NECTIN-4 FRAGMENT D1-D2
4fs0 CRYSTAL STRUCTURE OF MUTANT F136D OF MOUSE NECTIN-2 FRAGMENT D1-D2