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(-) Description

Title :  CRYSTAL STRUCTURE OF HLA-DQ2.5-CLIP2
 
Authors :  T. B. Nguyen, P. Jayaraman, E. Bergseng, M. S. Madhusudhan, C. -Y. Kim, L
Date :  10 Jul 16  (Deposition) - 05 Apr 17  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hla-Dq2. 5, Clip2, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. B. Nguyen, P. Jayaraman, E. Bergseng, M. S. Madhusudhan, C. -Y. Kim, L. M. Sollid
Structural Basis For The Class-Ii-Associated Invariant Chai Peptide-Rich Phenotype Of Human Leukocyte Antigen Dq2. 5
J. Biol. Chem. 2017
PubMed: search  |  Reference-DOI: 10.1074/JBC.M117.785139

(-) Compounds

Molecule 1 - MHC CLASS II HLA-DQ-ALPHA CHAIN
    ChainsA
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System Taxid10469
    Expression System Vector TypeBACULOVIRUS
    FragmentUNP RESIDUES 1-193
    GeneHLA-DQA1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - MHC CLASS II HLA-DQ-BETA-1
    ChainsB
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System Taxid10469
    Expression System Vector TypeBACULOVIRUS
    FragmentUNP RESIDUES 1-198
    GeneHLA-DQB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 3 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN
    ChainsC
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System Taxid10469
    Expression System Vector TypeBACULOVIRUS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5KSV)

(-) Sites  (0, 0)

(no "Site" information available for 5KSV)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:107 -A:163
2B:15 -B:79
3B:117 -B:173

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Tyr A:9 -Gly A:9A
2Gly A:17 -Pro A:18
3Phe A:113 -Pro A:114
4Tyr B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5KSV)

(-) 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:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeeeeee....eeeeeeee..eeeeeee....eeee.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee.......eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ksv A   1 IVADHVASYGVNLYQSYGPSGQYTHEFDGDEQFYVDLGRKETVWCLPVLRQFRFDPQFALTNIAVLKHNLNSLIKRSNSTAATNEVPEVTVFSKSPVTLGQPNILICLVDNIFPPVVNITWLSNGHSVTEGVSETSFLSKSDHSFFKISYLTLLPSAEESYDCKVEHWGLDKPLLKHWEP 180
                                    9A        19        29        39        49  ||    60        70        80        90       100       110       120       130       140       150       160       170       180
                                    9A                                         52|                                                                                                                              
                                                                                54                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ksv B   3 SPEDFVYQFKGMCYFTNGTERVRLVSRSIYNREEIVRFDSDVGEFRAVTLLGLPAAEYWNSQKDILERKRAAVDRVCRHNYQLELRTTLQRRVEPTVTISPSNLLVCSVTDFYPAQIKVRWFRNDQEETAGVVSTPLIRNGDWTFQILVMLEMTPQRGDVYTCHVEHPSLQSPITVEWRA 190
                                    12        22        32        42        52        62        72        82        92       102 ||    120       130       140       150       160       170       180       190
                                                                                                                               104|                                                                             
                                                                                                                                113                                                                             

Chain C from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5ksv C  -3 MATPLLMQALPM   9
                              ||     7  
                             -1|        
                               1        

   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 5KSV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (85, 127)

Asymmetric/Biological Unit(hide GO term definitions)

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(no "Sites" information available for 5ksv)
 
  Cis Peptide Bonds
    Gly A:17 - Pro A:18   [ RasMol ]  
    Phe A:113 - Pro A:114   [ RasMol ]  
    Tyr A:9 - Gly A:9A  [ RasMol ]  
    Tyr B:123 - Pro B:124   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        DQA1_HUMAN | P019091jk8 1nbn 1s9v 1uvq 2nna 4gg6 4ozf 4ozg 4ozh 4ozi 5ksa 5ksb 5ksu
        HG2A_HUMAN | P042331a6a 1icf 1iie 1l3h 1muj 3pdo 3pgc 3pgd 3qxa 3qxd 4aen 4ah2 4x5w 5ksu
        O19712_HUMAN | O197125ksu
        Q5Y7D3_HUMAN | Q5Y7D34d8p
UniProtKB/TrEMBL
        Q5Y7D3_HUMAN | Q5Y7D34ozf 4ozg 4ozh 4ozi 5ksu

(-) Related Entries Specified in the PDB File

5ksu