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(-) Description

Title :  STRUCTURE OF TIGIT BOUND TO NECTIN-2 (CD112)
 
Authors :  F. A. Deuss, B. S. Gully, J. Rossjohn, R. Berry
Date :  13 Mar 17  (Deposition) - 24 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Immune Receptor, Adhesion Molecule, Immunoglobulin Fold, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  F. A. Deuss, B. S. Gully, J. Rossjohn, R. Berry
Recognition Of Nectin-2 By The Natural Killer Cell Receptor Tigit.
J. Biol. Chem. 2017
PubMed-ID: 28515320  |  Reference-DOI: 10.1074/JBC.M117.786483

(-) Compounds

Molecule 1 - T-CELL IMMUNORECEPTOR WITH IG AND ITIM DOMAINS
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: TIGIT, VSIG9, VSTM3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: V-SET AND IMMUNOGLOBULIN DOMAIN-CONTAINING PROTEIN 9,V-SET AND TRANSMEMBRANE DOMAIN-CONTAINING PROTEIN 3
 
Molecule 2 - NECTIN-2
    Chains: C, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Gene: NECTIN2, HVEB, PRR2, PVRL2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HERPES VIRUS ENTRY MEDIATOR B,HVEB,NECTIN CELL ADHESION MOLECULE 2,POLIOVIRUS RECEPTOR-RELATED PROTEIN 2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
3SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:64 , SER A:78 , PRO A:79 , SER A:80binding site for residue GOL A 200
2AC2SOFTWAREGLN B:64 , SER B:78 , PRO B:79 , SER B:80binding site for residue SO4 B 201
3AC3SOFTWAREASP C:74 , ASN C:137 , MET C:153 , TRP C:155binding site for Mono-Saccharide NAG C 200 bound to ASN C 137

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:45 -A:108
2B:45 -B:108
3C:54 -C:140
4D:54 -D:140

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Gly A:88 -Pro A:89
2Tyr A:113 -Pro A:114
3Gly B:88 -Pro B:89
4Tyr B:113 -Pro B:114
5Leu C:57 -Pro C:58
6Lys C:97 -Pro C:98
7Phe C:145 -Pro C:146
8Leu D:57 -Pro D:58
9Lys D:97 -Pro D:98
10Phe D:145 -Pro D:146

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V52)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V52)

(-) Exons   (0, 0)

(no "Exon" information available for 5V52)

(-) 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:103
                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee......eee.eeee....eeeeeeeee..eeeeeee...eeee.......eee.....eee...hhhhheeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 5v52 A  24 TGTIETTGNISAEKGGSIILQCHLSSTTAQVTQVNWEQQDQLLAISNADLGWHISPSFKDRVAPGPGLGLTLQSLTVNDTGEYFCIYHTYPDGTYTGRIFLEV 126
                                    33        43        53        63        73        83        93       103       113       123   


Chain B from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eee.eeee....eeeeeeeee..eeeeeee...eeee.......eee.....eee...hhhhheeeeeeeeee..eeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5v52 B  24 TGTIETTGNISAEKGGSIILQCHLSSTTAQVTQVNWEQQDQLLAISNADLGWHISPSFKDRVAPGPGLGLTLQSLTVNDTGEYFCIYHTYPDGTYTGRIFLEVL 127
                                    33        43        53        63        73        83        93       103       113       123    


Chain C from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eee.eeee......eeeeeeee....hhhh.eeeeee...eee..........eee................eee...hhhhheeeeeeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v52 C  33 DVRVQVLPEVRGQLGGTVELPCHLLPPVPGLYISLVTWQRPDAPANHQNVAAFHPKMGPSFPSPKPGSERLSFVSAKQSTTEAELQDATLALHGLTVEDEGNYTCEFATFPKGSVRGMTWLRVLV 160
                                    42        52        62        72        82        92       102       112|      125       135       145       155     
                                                                                                         112|                                            
                                                                                                          116                                            


Chain D from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eee.eeee......eeeeeeee....hhhh.eeeeee...eee..........eee................eee...hhhhheeeeeeeeee..eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v52 D  33 DVRVQVLPEVRGQLGGTVELPCHLLPPVPGLYISLVTWQRPDAPANHQNVAAFHPKMGPSFPSPKPGSERLSFVSAKQSTTEAELQDATLALHGLTVEDEGNYTCEFATFPKGSVRGMTWLRVLVPR 162
                                    42        52        62        72        82        92       102       112|      125       135       145       155       
                                                                                                         112|                                              
                                                                                                          116
   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 5V52)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V52)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V52)

(-) Gene Ontology  (50, 63)

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  5v52
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  TIGIT_HUMAN | Q495A1
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 Related Entries

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

UniProtKB/Swiss-Prot
        NECT2_HUMAN | Q92692: 3r0n 4dfh 4dfi 4hza
        TIGIT_HUMAN | Q495A1: 3q0h 3rq3 3ucr 3udw

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