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(-) Description

Title :  HLA-DR1 WITH CLIP102-120(M107W)
 
Authors :  S. Guenther, C. Freund
Date :  06 Dec 14  (Deposition) - 09 Mar 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.34
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Mhc Ii, Immune System, Self Antigen, Invariant Chain, Clip (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Wieczorek, J. Sticht, S. Stolzenberg, S. Gunther, C. Wehmeyer, Z. El Habre, M. Alvaro-Benito, F. Noe, C. Freund
Mhc Class Ii Complexes Sample Intermediate States Along The Peptide Exchange Pathway.
Nat Commun V. 7 13224 2016
PubMed-ID: 27827392  |  Reference-DOI: 10.1038/NCOMMS13224

(-) Compounds

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET11A
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR, UNP RESIDUES 26-217
    Gene: HLA-DRA, HLA-DRA1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DRA
 
Molecule 2 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET24D
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EXTRACELLULAR, UNP RESIDUES 30-227
    Gene: HLA-DRB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DRB1*1,DR1
 
Molecule 3 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN GAMMA CHAIN
    Chains: C
    Engineered: YES
    Fragment: EXTRACELLULAR, UNP RESIDUES 102-120
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HLA-DR ANTIGENS-ASSOCIATED INVARIANT CHAIN,IA ANTIGEN- ASSOCIATED INVARIANT CHAIN,II,P33
    Synthetic: YES

 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 4X5W)

(-) Sites  (0, 0)

(no "Site" information available for 4X5W)

(-) SS Bonds  (3, 3)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Asn A:15 -Pro A:16
2Thr A:113 -Pro A:114
3Tyr B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X5W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X5W)

(-) Exons   (0, 0)

(no "Exon" information available for 4X5W)

(-) 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:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhh.ee..hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee.......eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x5w A   0 MIKEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEF 180
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179 


Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee...eeeeeeee.....eeeeee..eee...eee...ee.....eeeeeee........eeeeeee.......eeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4x5w B   2 DTRPRFLWQLKFECHFFNGTERVRLLERCIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSESAQSK 198
                                    11        21        31        41        51        61        71        81        91       101  ||   120       130       140       150       160       170       180       190        
                                                                                                                                104|                                                                                    
                                                                                                                                 114                                                                                    


Chain C from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .ee............ Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 4x5w C 104 VSKWRMATPLLMQAL 118
                                   113
   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 4X5W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X5W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X5W)

(-) Gene Ontology  (102, 158)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:15 - Pro A:16   [ RasMol ]  
    Thr A:113 - Pro A:114   [ 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
        2B11_HUMAN | P04229: 1aqd 1bx2 1dlh 1fyt 1hxy 1jwm 1jws 1jwu 1kg0 1klg 1klu 1lo5 1pyw 1r5i 1seb 1sje 1sjh 1t5w 1t5x 2fse 2g9h 2iam 2ian 2icw 2ipk 2oje 2xn9 3l6f 3pdo 3pgc 3pgd 3qxa 3qxd 3s4s 3s5l 4aen 4ah2 4c56 4e41 4fqx 4gbx 4i5b 4ov5 4x5x 5v4n
        DRA_HUMAN | P01903: 1a6a 1aqd 1bx2 1d5m 1d5x 1d5z 1d6e 1dlh 1fv1 1fyt 1h15 1hqr 1hxy 1j8h 1jwm 1jws 1jwu 1kg0 1klg 1klu 1lo5 1pyw 1r5i 1seb 1sje 1sjh 1t5w 1t5x 1ymm 1zgl 2fse 2g9h 2iam 2ian 2icw 2ipk 2oje 2q6w 2seb 2wbj 2xn9 3c5j 3l6f 3o6f 3pdo 3pgc 3pgd 3qxa 3qxd 3s4s 3s5l 3t0e 4aen 4ah2 4c56 4e41 4fqx 4gbx 4h1l 4h25 4h26 4i5b 4is6 4mcy 4mcz 4md0 4md4 4md5 4mdi 4mdj 4ov5 4x5x 4y19 4y1a 5jlz 5lax 5v4m 5v4n
        HG2A_HUMAN | P04233: 1a6a 1icf 1iie 1l3h 1muj 3pdo 3pgc 3pgd 3qxa 3qxd 4aen 4ah2 5ksu 5ksv

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4X5W)