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(-) Description

Title :  CRYSTAL STRUCTURE OF MOUSE NECTIN-2 EXTRACELLULAR FRAGMENT D1-D2, 2ND CRYSTAL FORM
 
Authors :  O. J. Harrison, J. Brasch, L. Shapiro
Date :  18 Jun 12  (Deposition) - 22 Aug 12  (Release) - 26 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.35
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (2x)
Biol. Unit 2:  B,C  (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 2
    Chains: A, B, C
    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

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): A  
Biological Unit 2 (1x):  BC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
1BMA5Ligand/IonBETA-D-MANNOSE
2FUC5Ligand/IonALPHA-L-FUCOSE
3NAG11Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1BMA4Ligand/IonBETA-D-MANNOSE
2FUC4Ligand/IonALPHA-L-FUCOSE
3NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (3, 13)
No.NameCountTypeFull Name
1BMA3Ligand/IonBETA-D-MANNOSE
2FUC3Ligand/IonALPHA-L-FUCOSE
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:126 , GLY A:127 , ASN A:128 , TRP A:146 , NAG A:302 , FUC A:304 , ARG B:221BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWARETRP A:146 , NAG A:301 , BMA A:303 , FUC A:304BINDING SITE FOR RESIDUE NAG A 302
03AC3SOFTWARENAG A:302BINDING SITE FOR RESIDUE BMA A 303
04AC4SOFTWARENAG A:301 , NAG A:302BINDING SITE FOR RESIDUE FUC A 304
05AC5SOFTWAREARG A:35 , GLU A:62 , ASN A:138 , ARG A:141 , NAG A:306 , FUC A:308BINDING SITE FOR RESIDUE NAG A 305
06AC6SOFTWARETHR A:61 , NAG A:305 , BMA A:307 , FUC A:308BINDING SITE FOR RESIDUE NAG A 306
07AC7SOFTWARENAG A:306BINDING SITE FOR RESIDUE BMA A 307
08AC8SOFTWAREPRO A:89 , NAG A:305 , NAG A:306BINDING SITE FOR RESIDUE FUC A 308
09AC9SOFTWAREASN B:128 , TRP B:146 , NAG B:302 , FUC B:304BINDING SITE FOR RESIDUE NAG B 301
10BC1SOFTWARETRP B:146 , NAG B:301 , BMA B:303 , FUC B:304BINDING SITE FOR RESIDUE NAG B 302
11BC2SOFTWARENAG B:302BINDING SITE FOR RESIDUE BMA B 303
12BC3SOFTWARENAG B:301 , NAG B:302BINDING SITE FOR RESIDUE FUC B 304
13BC4SOFTWAREARG B:35 , GLU B:62 , ASN B:138 , ARG B:141 , NAG B:306 , FUC B:308BINDING SITE FOR RESIDUE NAG B 305
14BC5SOFTWARENAG B:305 , BMA B:307 , FUC B:308BINDING SITE FOR RESIDUE NAG B 306
15BC6SOFTWARENAG B:306BINDING SITE FOR RESIDUE BMA B 307
16BC7SOFTWARENAG B:305 , NAG B:306 , PRO C:89BINDING SITE FOR RESIDUE FUC B 308
17BC8SOFTWAREASN C:128 , NAG C:302 , FUC C:304BINDING SITE FOR RESIDUE NAG C 301
18BC9SOFTWARENAG C:301 , BMA C:303BINDING SITE FOR RESIDUE NAG C 302
19CC1SOFTWARENAG C:302BINDING SITE FOR RESIDUE BMA C 303
20CC2SOFTWARENAG C:301BINDING SITE FOR RESIDUE FUC C 304
21CC3SOFTWARETHR C:61 , GLU C:62 , ASN C:138 , ARG C:141BINDING SITE FOR RESIDUE NAG C 305

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:131 -A:54
2A:229 -A:174
3B:131 -B:54
4B:229 -B:174
5C:131 -C:54
6C:229 -C:174

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Pro A:58 -Pro A:59
2Phe A:136 -Pro A:137
3Arg A:180 -Pro A:181
4Pro B:58 -Pro B:59
5Phe B:136 -Pro B:137
6Arg B:180 -Pro B:181
7Pro C:58 -Pro C:59
8Thr C:107 -Asn C:108
9Phe C:136 -Pro C:137
10Arg C:180 -Pro C:181

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FN0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FN0)

(-) Exons   (0, 0)

(no "Exon" information available for 4FN0)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eee.eee......eeeeeeeee....eeeeee...eee..........eee...............eee...hhhhheeeeeeeeee..eeeeeeeeeeee...eeeeee.........eeeeeeeeeee....eeeee......eeee.........eeeeeeeee..hhhhh..eeeeeee.......eeeeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fn0 A  32 QDVRVRVLPEVRGRLGGTVELPCHLLPPTTERVSQVTWQRLDGTVVAAFHPSFGVDFPNSQFSKDRLSFVRARPETNADLRDATLAFRGLRVEDEGNYTCEFATFPNGTRRGVTWLRVIAQPENHAEAQEVTIGPQSVAVARCVSTGGRPPARITWISSLGGEAKDTQEPGIQAGTVTIISRYSLVPVGRADGVKVTCRVEHESFEEPILLPVTLSVRYH 251
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee....eee.eee......eeeeeeeee....eeeeee...eee..hhhhh...eee...............eee...hhhhheeeeeeeeee..eeeeeeeeeeee...eeeeee.eee.....eeeeeeeeeee....eeeee......eeeeeee......eeeeeeeee..hhhhh..eeeeeee.......eeeeee.eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fn0 B  32 QDVRVRVLPEVRGRLGGTVELPCHLLPPTTERVSQVTWQRLDGTVVAAFHPSFGVDFPNSQFSKDRLSFVRARPETNADLRDATLAFRGLRVEDEGNYTCEFATFPNGTRRGVTWLRVIAQPENHAEAQEVTIGPQSVAVARCVSTGGRPPARITWISSLGGEAKDTQEPGIQAGTVTIISRYSLVPVGRADGVKVTCRVEHESFEEPILLPVTLSVRYH 251
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251


Chain C from PDB  Type:PROTEIN  Length:219
                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee..eeeee...eeee.eee......eeeeeeeee....eeeeee...eee..hhhhh....ee...............eeee..hhhhheeeeeeeeee..eeeeeeeeeeee...eeeeee.........eeeeeeeeeee....eeeee......eeeeeee......eeeeeeeee..hhhhh..eeeeeee.......eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fn0 C  32 QDVRVRVLPEVRGRLGGTVELPCHLLPPTTERVSQVTWQRLDGTVVAAFHPSFGVDFPNSQFSKDRLSFVRARPETNADLRDATLAFRGLRVEDEGNYTCEFATFPNGTRRGVTWLRVIAQPENHAEAQEVTIGPQSVAVARCVSTGGRPPARITWISSLGGEAKDTQEPGIQAGTVTIISRYSLVPVGRADGVKVTCRVEHESFEEPILLPVTLSVRY 250
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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 4FN0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FN0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FN0)

(-) Gene Ontology  (40, 40)

Asymmetric Unit(hide GO term definitions)

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  NECT2_MOUSE | P32507
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 Related Entries

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        NECT2_MOUSE | P32507: 4fmk 4fs0

(-) Related Entries Specified in the PDB File

4fmf CRYSTAL STRUCTURE OF NECTIN-1
4fmk CRYSTAL STRUCTURE OF NECTIN-2