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(-) Description

Title :  CRYSTAL STRUCTURE OF AN IMMUNE COMPLEX AT PH 6.5
 
Authors :  D. K. Sethi, W. Pos, K. W. Wucherpfennig
Date :  28 Jul 12  (Deposition) - 16 Jan 13  (Release) - 16 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  C,D  (1x)
Biol. Unit 2:  A,B,E  (1x)
Keywords :  Immune Complex, Peptide Loading, Peptide Editing, Antigen Presentation, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Pos, D. K. Sethi, M. J. Call, M. S. Schulze, A. K. Anders, J. Pyrdol, K. W. Wucherpfennig
Crystal Structure Of The Hla-Dm-Hla-Dr1 Complex Defines Mechanisms For Rapid Peptide Selection.
Cell(Cambridge, Mass. ) V. 151 1557 2012
PubMed-ID: 23260142  |  Reference-DOI: 10.1016/J.CELL.2012.11.025

(-) Compounds

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DM ALPHA CHAIN
    Chains: C
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Plasmid: PEE14.1
    Expression System Strain: LEC3.2.8.1
    Expression System Taxid: 10029
    Expression System Vector Type: PLASMID
    Gene: ALPHA CHAIN, DMA, HLA-DM, HLA-DMA, MHC CLASS II MOLECULE, RING6
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DMA, REALLY INTERESTING NEW GENE 6 PROTEIN
 
Molecule 2 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DM BETA CHAIN
    Chains: D
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Plasmid: PEE14.1
    Expression System Strain: LEC3.2.8.1
    Expression System Taxid: 10029
    Expression System Vector Type: PLASMID
    Gene: BETA CHAIN, DMB, HLA-DMB, MHC CLASS II MOLECULE HLA-DM, RING7
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DMB, REALLY INTERESTING NEW GENE 7 PROTEIN
 
Molecule 3 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: ALPHA CHAIN, HLA-DR1, HLA-DRA, HLA-DRA1, MHC CLASS II MOLECULE
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DRA
 
Molecule 4 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-1 BETA CHAIN
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: BETA CHAIN, HLA-DR1, HLA-DRB1, MHC CLASS II MOLECULE
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DRB1*1, DR-1, DR1
 
Molecule 5 - SYNTHETIC PEPTIDE
    Chains: E
    Engineered: YES
    Organism Common: SYNTHETIC CONSTRUCT
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x):   CD 
Biological Unit 2 (1x): AB  E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN C:15 , LEU D:12 , LYS D:20BINDING SITE FOR RESIDUE NAG C 301
2AC2SOFTWAREVAL A:116 , ASN A:118 , TRP A:168BINDING SITE FOR RESIDUE NAG A 201
3AC3SOFTWAREASN A:78BINDING SITE FOR RESIDUE NAG A 202

(-) SS Bonds  (9, 9)

Asymmetric Unit
No.Residues
1A:65 -E:88
2A:107 -A:163
3B:15 -B:79
4B:117 -B:173
5C:24 -C:79
6C:121 -C:176
7D:11 -D:79
8D:25 -D:35
9D:117 -D:174

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Ser C:28 -Pro C:29
2Phe C:127 -Pro C:128
3Tyr D:123 -Pro D:124
4Asn A:15 -Pro A:16
5Gln A:57 -Gly A:58
6Thr A:113 -Pro A:114
7Tyr B:123 -Pro B:124

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GBX)

(-) 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..ee.....ee...ee.....eeeeeeeee.......eeeeee.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gbx A   3 EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIACDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDA 182
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182


Chain B from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeee......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gbx B  -5 VLFQGPGDTRPRFLWQLKFECHFFNGTERVRLLERSIYNQEESVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVGESFTVQRRVEPKVTVYPSHNLLVCSVSGFYPGSIEVRWFRNGQEEKAGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSVTSPLTVEWRA 190
                                     4        14        24        34        44        54        64        74        84        94       104|      121       131       141       151       161       171       181         
                                                                                                                                       104|                                                                              
                                                                                                                                        112                                                                              


Chain C from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.....eeeeeee..eeeeeee....eeee.............hhhhhhhhhhhhhhhhhhhhhhhh....ee....eeeeee.........eeeeeeeeee....eeeeeee..eee..eeeeeeeee...eeeeeeeeee.......eeeeeee.....eeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gbx C  12 DLQNHTFLHTVYCQDGSPSVGLSEAYDEDQLFFFDFSQNTRVPRLPEFADWAQEQGDAPAILFDKEFCEWMIQQIGPKLDGKIPVSRGFPIAEVFTLKPLEFGKPNTLVCFVSNLFPPMLTVNWQHHSVPVEGFGPTFVSAVDGLSFQAFSYLDFTPEPSDIFSCIVTHEIDRYTAIAYWVPRNALPSL 200
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191         


Chain D from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee.....eeeeeeeeee...eee................hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee.........eeeeeeeeee......eeeee..eee..........ee.....eeeeeeeee.......eeeee........eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gbx D   3 FVAHVESTCLLDDAGTPKDFTYCISFNKDLLTCWDPEENKMAPSEFGVLNSLANVLSQHLNQKDTLMQRLRNGLQNCATHTQPFWGSLTDRTRPPSVQVAKTTPFNTREPVMLACYVWGFYPAEVTITWRKNGKLVMPHSSAHKTAQPNGDWTYQTLSHLALTPSYGDTYTCVVEHIGAPEPILRDWTPGL 193
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192 


Chain E from PDB  Type:PROTEIN  Length:10
                                          
               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
                 4gbx E  84 GKQNCLKLAT  93
                                    93
   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 4GBX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (54, 115)

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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 4i5b 4ov5 4x5w 4x5x 5v4n
        DMA_HUMAN | P28067: 1hdm 2bc4 4fqx
        DMB_HUMAN | P28068: 1hdm 2bc4 4fqx 4i0p
        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 4h1l 4h25 4h26 4i5b 4is6 4mcy 4mcz 4md0 4md4 4md5 4mdi 4mdj 4ov5 4x5w 4x5x 4y19 4y1a 5jlz 5lax 5v4m 5v4n

(-) Related Entries Specified in the PDB File

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