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(-) Description

Title :  HLA-DO IN COMPLEX WITH HLA-DM
 
Authors :  A. I. Guce, S. E. Mortimer, L. J. Stern
Date :  18 Nov 12  (Deposition) - 26 Dec 12  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Hla-Dm, Hla-Do, Hla-Dr, Peptide Loading, Immune System, Inhibitor, Enzyme Hla-Dm (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. I. Guce, S. E. Mortimer, T. Yoon, C. A. Painter, W. Jiang, E. D. Mellins, L. J. Stern
Hla-Do Acts As A Substrate Mimic To Inhibit Hla-Dm By A Competitive Mechanism.
Nat. Struct. Mol. Biol. V. 20 90 2013
PubMed-ID: 23222639  |  Reference-DOI: 10.1038/NSMB.2460

(-) Compounds

Molecule 1 - HLA-DMA PROTEIN
    Chains: A, E
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Strain: SCHNEIDER-2
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Gene: 3108, HLA-DMA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HOMO SAPIENS
 
Molecule 2 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DM BETA CHAIN
    Chains: B, F
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Strain: SCHNEIDER-2
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Gene: 3109, DMB, HLA-DMB, RING7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HOMO SAPIENS
    Synonym: MHC CLASS II ANTIGEN DMB, REALLY INTERESTING NEW GENE 7 PROTEIN
 
Molecule 3 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DO ALPHA CHAIN
    Chains: C, G
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Strain: SCHNEIDER-2
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Gene: 3111, HLA-DNA, HLA-DOA, HLA-DZA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HOMO SAPIENS
    Synonym: MHC DN-ALPHA, MHC DZ ALPHA, MHC CLASS II ANTIGEN DOA
 
Molecule 4 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DO BETA CHAIN
    Chains: D, H
    Engineered: YES
    Expression System: DROSOPHILA MELANOGASTER
    Expression System Strain: SCHNEIDER-2
    Expression System Taxid: 7227
    Expression System Vector Type: PLASMID
    Gene: 3112, HLA-DOB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Strain: HOMO SAPIENS
    Synonym: MHC CLASS II ANTIGEN DOB

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL3Ligand/IonGLYCEROL
3NAG7Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1ACT-1Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:15 , LEU B:12BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWAREASN C:118 , GLU C:166 , TRP C:168BINDING SITE FOR RESIDUE NAG C 201
03AC3SOFTWAREASN D:19 , GLU D:22 , LYS D:23BINDING SITE FOR RESIDUE NAG D 201
04AC4SOFTWARELEU D:174BINDING SITE FOR RESIDUE GOL D 202
05AC5SOFTWAREASN E:15BINDING SITE FOR RESIDUE NAG E 301
06AC6SOFTWARELYS F:65BINDING SITE FOR RESIDUE GOL F 201
07AC7SOFTWAREASN G:78BINDING SITE FOR RESIDUE NAG G 201
08AC8SOFTWAREASN G:118 , GLU G:166BINDING SITE FOR RESIDUE NAG G 202
09AC9SOFTWAREASN H:19 , GLU H:22BINDING SITE FOR RESIDUE NAG H 201
10BC1SOFTWAREALA D:49 , THR D:51 , LYS D:52 , GLN D:55 , ALA H:49 , LYS H:52 , GLN H:55BINDING SITE FOR RESIDUE PGE H 202
11BC2SOFTWAREILE H:127 , SER H:144BINDING SITE FOR RESIDUE ACT H 203
12BC3SOFTWAREARG G:44 , LYS G:94 , ASP H:152BINDING SITE FOR RESIDUE GOL H 204

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:24 -A:79
2A:121 -A:176
3B:11 -B:79
4B:25 -B:35
5B:117 -B:174
6C:107 -C:163
7D:15 -D:79
8D:117 -D:173
9E:24 -E:79
10E:121 -E:176
11F:11 -F:79
12F:25 -F:35
13F:117 -F:174
14G:107 -G:163
15H:15 -H:79
16H:117 -H:173

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser A:28 -Pro A:29
2Phe A:127 -Pro A:128
3Tyr B:123 -Pro B:124
4Phe C:113 -Pro C:114
5Tyr D:123 -Pro D:124
6Arg D:189 -Ala D:190
7Ser E:28 -Pro E:29
8Phe E:127 -Pro E:128
9Ser E:199 -Asp E:200
10Tyr F:123 -Pro F:124
11Phe G:113 -Pro G:114
12Tyr H:123 -Pro H:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I0P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I0P)

(-) Exons   (0, 0)

(no "Exon" information available for 4I0P)

(-) 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:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeee..eeeeeee....eeee.hhhhhhhhh...hhhhhhhhhhhhhhhhhhh.........eee...eeeeee.........eeeeeeeeee....eeeeeee...ee......eeeee...eeeeeeeeee.......eeeeeee....eeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i0p A  13 LQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEIDRYTAIAYWVPRNALPSD 200
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192        


Chain B from PDB  Type:PROTEIN  Length:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeeeeee..eeeeeee....eeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee........eeeeeeeeee.....eeeeee...ee......ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i0p B   3 FVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCEFGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHKTAQPNGDWTYQTLSHLALTPSYGDTYTCVVEHIGAPEPILRDWTPG 192
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       146       156       166       176       186      
                                                                                                                                                                    141|                                              
                                                                                                                                                                     146                                              


Chain C from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee.hhheeeeeeee..eeeeeee....eeee.hhhhh..........hhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i0p C   2 KADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQ 181
                                   10A        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
                                   10A                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeeeee.....eeeeee..ee....ee....ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i0p D   4 PEDFVIQAKADCYFTNGTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVCRHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEERAGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWRAQ 191
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183        


Chain E from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee.....eeeeeee..eeeeeee....eeee.hhhhhhhh....hhhhhhhhhhhhhhhhhhh.........eee...eeeeee.........eeeeeeeeee....eeeeeee...ee.....eeeee.....eeeeeeeee.......eeeeeee....eeeeeee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i0p E  13 LQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLNFTPEPSDIFSCIVTHEIDRYTAIAYWVPRNALPSD 200
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192        


Chain F from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeeeeeee..eeeeeee....eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeeee........eeeeeeeeee.....eeeeee...ee......ee.....eeeeeeeee.......eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i0p F   3 FVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPCEFGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTNRTRPPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHKTAQPNGDWTYQTLSHLALTPSYGDTYTCVVEHIGAPEPILRDWTPGL 193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       146       156       166       176       186       
                                                                                                                                                                    141|                                               
                                                                                                                                                                     146                                               


Chain G from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee.hhheeeeeeee..eeeeeee....eeee.hhhhh..........hhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i0p G   2 KADHMGSYGPAFYQSYGASGQFTHEFDEEQLFSVDLKKSEAVWRLPEFGDFARFDPQGGLAGIAAIKAHLDILVERSNRSRAINVPPRVTVLPKSRVELGQPNILICIVDNIFPPVINITWLRNGQTVTEGVAQTSFYSQPDHLFRKFHYLPFVPSAEDVYDCQVEHWGLDAPLLRHWELQ 181
                                   10A        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180 
                                   10A                                                                                                                                                                           


Chain H from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.........eeeeeeeeee.....eeeeee..ee....eee...ee.....eeeeeeeee.......eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i0p H   4 PEDFVIQAKADCYFTNGTEKVQFVVRFIFNLEEYVRFDSDVGMFVALTKLGQPDAEQWNSRLDLLERSRQAVDGVCRHNYRLGAPFTVGRKVQPEVTVYPERTPLLHQHNLLHCSVTGFYPGDIKIKWFLNGQEERAGVMSTGPIRNGDWTFQTVVMLEMTPELGHVYTCLVDHSSLLSPVSVEWRAQS 192
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
   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 4I0P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I0P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I0P)

(-) Gene Ontology  (25, 60)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DMB_HUMAN | P28068: 1hdm 2bc4 4fqx 4gbx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4I0P)