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(-) Description

Title :  STRUCTURE OF HUMAN MHC CLASS II PROTEIN HLA-DR1 CARRYING AN INFLUENZA HEMAGGLUTININ PEPTIDE PARTIALLY FILLING THE BINDING GROOVE
 
Authors :  M. -S. E. D. Schulze
Date :  28 Nov 12  (Deposition) - 04 Dec 13  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.12
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Immunoglobulin Fold, Antigen Presentation, Peptide-Mhc Complex, Membrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Schulze, A. K. Anders, D. K. Sethi, M. J. Call
Disruption Of Hydrogen Bonds Between Major Histocompatibility Complex Class Ii And The Peptide N-Terminus Is Not Sufficient To Form A Human Leukocyte Antigen-Dm Receptive State Of Major Histocompatibility Complex Class Ii.
Plos One V. 8 69228 2013
PubMed-ID: 23976922  |  Reference-DOI: 10.1371/JOURNAL.PONE.0069228

(-) Compounds

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
    Chains: A, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    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, E
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: HLA-DRB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DRB1*1, DR-1, DR1
 
Molecule 3 - TRUNCATED HEMAGGLUTININ PEPTIDE
    Chains: C, F
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4I5B)

(-) Sites  (0, 0)

(no "Site" information available for 4I5B)

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:65 -C:313
2A:107 -A:163
3B:15 -B:79
4B:117 -B:173
5D:65 -F:313
6D:107 -D:163
7E:15 -E:79
8E:117 -E:173

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asn A:15 -Pro A:16
2Thr A:113 -Pro A:114
3Tyr B:123 -Pro B:124
4Asn D:15 -Pro D:16
5Thr D:113 -Pro D:114
6Tyr E:123 -Pro E:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I5B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I5B)

(-) Exons   (0, 0)

(no "Exon" information available for 4I5B)

(-) 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:180
                                                                                                                                                                                                                    
               SCOP domains d4i5ba1 A:2-81 Class II MHC alpha chain, N-terminal domain                      d4i5ba2 A:82-181 Class II MHC alpha chain, C-terminal domain                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i5b A   2 KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIACDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                
               SCOP domains d4i5bb1 B:2-92 Class II MHC beta chain, N-terminal domain                                  d4i5bb2 B:93-193 Class II MHC beta chain, C-terminal domain                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i5b B   2 DTRPRFLWQLKFECHFFNGTERVRLLERSIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRARSE 193
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191  


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
                 4i5b C 308 VVKQNCLKLATK 319
                                   317  


Chain D from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains d4i5bd1 D:2-81 Class II MHC alpha chain, N-terminal domain                      d4i5bd2 D:82-188 Class II MHC alpha chain, C-terminal domain                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i5b D   2 KEEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIACDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDAPSPLPE 188
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       


Chain E from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                              
               SCOP domains d4i5be1 E:2-92 Class II MHC beta chain, N-terminal domain                                  d4i5be2 E:93-191 Class II MHC beta chain, C-terminal domain                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee......eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i5b E   2 DTRPRFLWQLKFECHFFNGTERVRLLERSIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSKTQPLQHHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRAR 191
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191


Chain F from PDB  Type:PROTEIN  Length:11
                                           
               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
                 4i5b F 308 VVKQNCLKLAT 318
                                   317
   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  (4, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I5B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I5B)

(-) Gene Ontology  (51, 82)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:15 - Pro A:16   [ RasMol ]  
    Asn D:15 - Pro D:16   [ RasMol ]  
    Thr A:113 - Pro A:114   [ 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 4ov5 4x5w 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 4is6 4mcy 4mcz 4md0 4md4 4md5 4mdi 4mdj 4ov5 4x5w 4x5x 4y19 4y1a 5jlz 5lax 5v4m 5v4n

(-) Related Entries Specified in the PDB File

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