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(-) Description

Title :  STRUCTURE OF HLA-DR15 WITH BOUND ALPHA3(135-145) PEPTIDE
 
Authors :  J. Petersen, J. Rossjohn
Date :  10 Mar 17  (Deposition) - 03 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,C,D,F,G,I,J,L
Biol. Unit 1:  D,F  (1x)
Biol. Unit 2:  A,C  (1x)
Biol. Unit 3:  G,I  (1x)
Biol. Unit 4:  J,L  (1x)
Keywords :  Hla-Dr, Immune Complex, Antigen Presenation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. D. Ooi, J. Petersen, Y. H. Tan, M. Huynh, Z. J. Willett, S. H. Ramarathinam, P. J. Eggenhuizen, K. L. Loh, K. A. Watson, P. Y. Gan M. A. Alikhan, N. L. Dudek, A. Handel, B. G. Hudson, L. Fugger, D. A. Power, S. G. Holt, P. T. Coates, J. W. Gregersen, A. W. Purcell, S. R. Holdsworth, N. L. La Gruta, H. H. Reid, J. Rossjohn, A. R. Kitchin
Dominant Protection From Hla-Linked Autoimmunity By Antigen-Specific Regulatory T Cells.
Nature V. 545 243 2017
PubMed-ID: 28467828  |  Reference-DOI: 10.1038/NATURE22329

(-) Compounds

Molecule 1 - HLA-DRA1
    Chains: D, A, G, J
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: HLA-DRA, HLA-DRA1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DRA
 
Molecule 2 - ALPHA3(135-145)-HLA-DRB1*15:01
    Chains: F, C, I, L
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Taxid: 7111
    Gene: HLA-DRB1, HLA-DRB2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DW2.2/DR2.2,MHC CLASS II ANTIGEN DRB1*15,DW2.2/DR2.2,MHC CLASS II ANTIGEN DRB1*15, CHIMERIC CONSTRUCT,DW2.2/DR2.2,MHC CLASS II ANTIGEN DRB1*15, CHIMERIC CONSTRUCT

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ACDFGIJL
Biological Unit 1 (1x):   DF    
Biological Unit 2 (1x): AC      
Biological Unit 3 (1x):     GI  
Biological Unit 4 (1x):       JL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1FUC4Ligand/IonALPHA-L-FUCOSE
2NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1FUC-1Ligand/IonALPHA-L-FUCOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1FUC-1Ligand/IonALPHA-L-FUCOSE
2NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:78 , LYS J:126binding site for Mono-Saccharide NAG A 201 bound to ASN A 78
2AC2SOFTWAREASN A:118 , TRP A:168 , ASP C:249binding site for Poly-Saccharide residues NAG A 202 through NAG A 203 bound to ASN A 118
3AC3SOFTWAREARG D:76 , ASN D:78 , HOH D:336 , LYS G:126 , PRO G:127binding site for Poly-Saccharide residues NAG D 201 through FUC D 203 bound to ASN D 78
4AC4SOFTWAREASN D:118 , GLU D:166 , TRP D:168binding site for Mono-Saccharide NAG D 204 bound to ASN D 118
5AC5SOFTWAREPRO D:127 , ARG G:76 , ASN G:78 , HOH G:310binding site for Poly-Saccharide residues NAG G 201 through FUC G 203 bound to ASN G 78
6AC6SOFTWAREASN G:118 , TRP G:168binding site for Poly-Saccharide residues NAG G 204 through NAG G 205 bound to ASN G 118
7AC7SOFTWARELYS A:126 , ASN J:78binding site for Mono-Saccharide NAG J 201 bound to ASN J 78
8AC8SOFTWAREASN J:118 , GLU J:166 , HIS J:167 , TRP J:168binding site for Mono-Saccharide NAG J 202 bound to ASN J 118

(-) SS Bonds  (12, 12)

Asymmetric Unit
No.Residues
1A:107 -A:163
2C:262 -C:326
3C:364 -C:420
4D:107 -D:163
5F:262 -F:326
6F:364 -F:420
7G:107 -G:163
8I:262 -I:326
9I:364 -I:420
10J:107 -J:163
11L:262 -L:326
12L:364 -L:420

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Asn D:15 -Pro D:16
2Thr D:113 -Pro D:114
3Tyr F:370 -Pro F:371
4Asn A:15 -Pro A:16
5Thr A:113 -Pro A:114
6Tyr C:370 -Pro C:371
7Asn G:15 -Pro G:16
8Thr G:113 -Pro G:114
9Tyr I:370 -Pro I:371
10Asn J:15 -Pro J:16
11Thr J:113 -Pro J:114
12Tyr L:370 -Pro L:371

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V4M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V4M)

(-) Exons   (0, 0)

(no "Exon" information available for 5V4M)

(-) 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:178
                                                                                                                                                                                                                  
               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....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v4m A   4 EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        


Chain C from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v4m C  -2 GWISLWKGFSFDTRPRFLWQPKRECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVESFTVQRRVQPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 437
                                     7||     257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
                                      8|                                                                                                                                                                                            
                                     249                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               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....ee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v4m D   4 EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        


Chain F from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v4m F  -2 GWISLWKGFSFDTRPRFLWQPKRECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVESFTVQRRVQPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 437
                                     7||     257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
                                      8|                                                                                                                                                                                            
                                     249                                                                                                                                                                                            


Chain G from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               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....ee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v4m G   4 EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        


Chain I from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v4m I  -2 GWISLWKGFSFDTRPRFLWQPKRECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVESFTVQRRVQPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 437
                                     7||     257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
                                      8|                                                                                                                                                                                            
                                     249                                                                                                                                                                                            


Chain J from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               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....ee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v4m J   4 EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        


Chain L from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5v4m L  -2 GWISLWKGFSFDTRPRFLWQPKRECHFFNGTERVRFLDRYFYNQEESVRFDSDVGEFRAVTELGRPDAEYWNSQKDILEQARAAVDTYCRHNYGVVESFTVQRRVQPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFLNGQEEKAGMVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 437
                                     7||     257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437
                                      8|                                                                                                                                                                                            
                                     249
   Legend:   → Mismatch (orange background)
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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 5V4M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V4M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V4M)

(-) Gene Ontology  (37, 69)

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  5v4m
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  DRA_HUMAN | P01903
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 Related Entries

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

UniProtKB/Swiss-Prot
        2B1F_HUMAN | P01911: 1bx2 1ymm 2wbj
        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 4x5w 4x5x 4y19 4y1a 5jlz 5lax 5v4n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5V4M)