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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT F136D OF MOUSE NECTIN-2 EXTRACELLULAR FRAGMENT D1-D2
 
Authors :  O. J. Harrison, J. Brasch, L. Shapiro
Date :  26 Jun 12  (Deposition) - 22 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym./Biol. Unit :  A
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
    Mutation: YES
    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/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:128 , SER A:190 , GLY A:192 , NAG A:302 , FUC A:303BINDING SITE FOR RESIDUE NAG A 301
2AC2SOFTWARENAG A:301 , FUC A:303BINDING SITE FOR RESIDUE NAG A 302
3AC3SOFTWARELEU A:72 , NAG A:301 , NAG A:302BINDING SITE FOR RESIDUE FUC A 303
4AC4SOFTWAREHIS A:55 , ARG A:112 , HIS A:156 , GLU A:158 , ARG A:173 , VAL A:175BINDING SITE FOR RESIDUE SO4 A 304

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asp A:136 -Pro A:137
2Asn A:138 -Gly A:139
3Arg A:180 -Pro A:181

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FS0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FS0)

(-) Exons   (0, 0)

(no "Exon" information available for 4FS0)

(-) 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:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eeeee....eee..ee.......eeeeeeee....eeeeee...eee..........eee......hhhhhh...eee...hhhhheeeeeeeee.....eeeeeeeeee...eeeeee.........eeeeeeeeeee....eeeee.....eeeeeeee......eeeeeeeee.........eeeeeee.......eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fs0 A  33 DVRVRVLPEVRGRLGGTVELPCHLLPPTTERVSQVTWQRLDGTVVAAFHPSFGVDFPNSQFSKDRLSFVRARPETNADLRDATLAFRGLRVEDEGNYTCEFATDPNGTRRGVTWLRVIAQPENHAEAQEVTIGPQSVAVARCVSTGGRPPARITWISSLGGEAKDTQEPGIQAGTVTIISRYSLVPVGRADGVKVTCRVEHESFEEPILLPVTLSVRY 250
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242
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  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 4FS0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FS0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FS0)

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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    Asp A:136 - Pro A:137   [ RasMol ]  
 

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  4fs0
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  NECT2_MOUSE | P32507
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 Related Entries

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

UniProtKB/Swiss-Prot
        NECT2_MOUSE | P32507: 4fmk 4fn0

(-) Related Entries Specified in the PDB File

4fmf CRYSTAL STRUCTURE OF HUMAN NECTIN-1 FULL ECTODOMAIN D1-D3
4fmk CRYSTAL STRUCTURE OF MURINE NECTIN-2 FRAGMENT D1-D2
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
4frw CRYSTAL STRUCTURE OF HUMAN NECTIN-4 FRAGMENT D1-D2