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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE NECTIN-2 EXTRACELLULAR FRAGMENT D1-D2
 
Authors :  O. J. Harrison, J. Brasch, L. Shapiro
Date :  17 Jun 12  (Deposition) - 22 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
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 2
    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: EXTRACELLULAR DOMAIN (D1-D2, UNP RESIDUES 32-250)
    Gene: PVRL2, MPH, PVR, PVS
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: NECTIN-2, HERPES VIRUS ENTRY MEDIATOR B, HERPESVIRUS ENTRY MEDIATOR B, HVEB, MURINE HERPES VIRUS ENTRY PROTEIN B, MHVEB, POLIOVIRUS RECEPTOR HOMOLOG

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric Unit (5, 15)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2CD4Ligand/IonCADMIUM ION
3FUC2Ligand/IonALPHA-L-FUCOSE
4MAN3Ligand/IonALPHA-D-MANNOSE
5NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (4, 22)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2CD-1Ligand/IonCADMIUM ION
3FUC4Ligand/IonALPHA-L-FUCOSE
4MAN6Ligand/IonALPHA-D-MANNOSE
5NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:61 , GLU A:62 , PRO A:89 , ASN A:138 , NAG A:302 , FUC A:306BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWAREASN A:90 , SER A:91 , NAG A:301 , BMA A:303BINDING SITE FOR RESIDUE NAG A 302
03AC3SOFTWARENAG A:302 , MAN A:304 , MAN A:305BINDING SITE FOR RESIDUE BMA A 303
04AC4SOFTWARESER A:91 , GLN A:92 , BMA A:303BINDING SITE FOR RESIDUE MAN A 304
05AC5SOFTWAREBMA A:303BINDING SITE FOR RESIDUE MAN A 305
06AC6SOFTWARETHR A:75 , NAG A:301BINDING SITE FOR RESIDUE FUC A 306
07AC7SOFTWAREASN A:128 , TRP A:146 , NAG A:308 , FUC A:311BINDING SITE FOR RESIDUE NAG A 307
08AC8SOFTWARENAG A:307 , BMA A:309 , FUC A:311BINDING SITE FOR RESIDUE NAG A 308
09AC9SOFTWARENAG A:308 , MAN A:310BINDING SITE FOR RESIDUE BMA A 309
10BC1SOFTWAREBMA A:309BINDING SITE FOR RESIDUE MAN A 310
11BC2SOFTWARENAG A:307 , NAG A:308BINDING SITE FOR RESIDUE FUC A 311
12BC3SOFTWAREHIS A:156 , GLU A:158 , GLU A:161 , ARG A:173 , ARG A:249BINDING SITE FOR RESIDUE CD A 312
13BC4SOFTWAREASP A:223 , HIS A:252 , HOH A:418 , HOH A:419BINDING SITE FOR RESIDUE CD A 313
14BC5SOFTWAREHIS A:55 , ASP A:113BINDING SITE FOR RESIDUE CD A 314
15BC6SOFTWAREASP A:110 , HIS A:251 , HOH A:433BINDING SITE FOR RESIDUE CD A 315

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:54 -A:131
2A:174 -A:229

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Pro A:58 -Pro A:59
2Phe A:136 -Pro A:137
3Arg A:180 -Pro A:181

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4FMK)

(-) 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:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeeee....eee..ee......eeeeeeee.....eeeeee...eee..........eee...............eee...hhhhheeeeeeeeee..eeeeeeeeeeee...eeeeee.........eeeeeeeeeee....eeeee.....eeeeeeee......eeeeeeeee..hhhhh..eeeeeee.......eeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fmk A  33 DVRVRVLPEVRGRLGGTVELPCHLLPPTTERVSQVTWQRLDGTVVAAFHPSFGVDFPNSQFSKDRLSFVRARPETNADLRDATLAFRGLRVEDEGNYTCEFATFPNGTRRGVTWLRVIAQPENHAEAQEVTIGPQSVAVARCVSTGGRPPARITWISSLGGEAKDTQEPGIQAGTVTIISRYSLVPVGRADGVKVTCRVEHESFEEPILLPVTLSVRYHHH 253
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
   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 4FMK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (40, 40)

Asymmetric Unit(hide GO term definitions)

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  4fmk
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  NECT2_MOUSE | P32507
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 Related Entries

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        NECT2_MOUSE | P32507: 4fn0 4fs0

(-) Related Entries Specified in the PDB File

4fmf CRYSTAL STRUCTURE OF NECTIN-1
4fn0 CRYSTAL STRUCTURE OF NECTIN-2, 2ND CRYSTAL FORM