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(-) Description

Title :  IMMUNE RECEPTOR
 
Authors :  S. W. Scally, J. Rossjohn
Date :  22 Aug 13  (Deposition) - 04 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hla-Dr, Antigen Presentation, T-Cell Receptor, Citrullination, Membrane, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Scally, J. Petersen, S. C. Law, N. L. Dudek, H. J. Nel, K. L. Loh, L. C. Wijeyewickrema, S. B. Eckle, J. Van Heemst, R. N. Pike, J. Mccluskey, R. E. Toes, N. L. La Gruta, A. W. Purcell, H. H. Reid, R. Thomas, J. Rossjohn
A Molecular Basis For The Association Of The Hla-Drb1 Locus Citrullination, And Rheumatoid Arthritis.
J. Exp. Med. V. 210 2569 2013
PubMed-ID: 24190431  |  Reference-DOI: 10.1084/JEM.20131241

(-) Compounds

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 26-206
    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, DRB1-4 BETA CHAIN
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Fragment: EXTRACELLULAR DOMAIN, UNP RESIDUES 30-219
    Gene: HLA-DRB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DRB1*4, DR-4, DR4
 
Molecule 3 - AGGRECAN CORE PROTEIN
    Chains: C
    Engineered: YES
    Fragment: UNP RESIDUES 89-103
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THIS SEQUENCE IS FROM HUMAN AGGRECAN AND CONTAINS CITRULLINE AT POSITIONS 93 AND 95
    Synonym: CARTILAGE-SPECIFIC PROTEOGLYCAN CORE PROTEIN, CSPCP, CHONDROITIN SULFATE PROTEOGLYCAN CORE PROTEIN 1, CHONDROITIN SULFATE PROTEOGLYCAN 1, AGGRECAN CORE PROTEIN 2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CIR2Mod. Amino AcidCITRULLINE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:110 , ARG A:140 , ARG A:146BINDING SITE FOR RESIDUE EDO A 204
2AC2SOFTWAREARG A:123 , ASN A:124BINDING SITE FOR RESIDUE EDO A 205
3AC3SOFTWAREVAL A:97 , GLU A:98 , HOH A:425 , HOH A:462BINDING SITE FOR RESIDUE EDO A 206
4AC4SOFTWAREASN A:78 , LYS A:126 , HOH A:516 , HOH A:527 , HOH A:540BINDING SITE FOR MONO-SACCHARIDE NAG A 201 BOUND TO ASN A 78
5AC5SOFTWAREASN A:118 , TRP A:168 , HOH A:389 , HOH A:501 , ASP B:2 , GLN C:13BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 118 RESIDUES 202 TO 203
6AC6SOFTWAREASN B:19 , GLU B:22BINDING SITE FOR MONO-SACCHARIDE NAG B 500 BOUND TO ASN B 19

(-) 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 4MD4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MD4)

(-) Exons   (0, 0)

(no "Exon" information available for 4MD4)

(-) 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:182
                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee...eeeeeeee..eeeeeee....eeee...hhhhhh...hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4md4 A   3 EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDTSG 184
                                    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.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.........eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.......eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4md4 B   2 DTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSLTSPLTVEWRA 190
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         


Chain C from PDB  Type:PROTEIN  Length:13
                                             
               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
                 4md4 C   1 ATEYrVrVNSAYQ  13
                                | | 10   
                                5-CIR    
                                  7-CIR
   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 4MD4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MD4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MD4)

(-) Gene Ontology  (69, 101)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        2B14_HUMAN | P13760: 1d5m 1d5x 1d5z 1d6e 1j8h 2seb 3o6f 3t0e 4is6 4mcy 4mcz 4md0 4md5 4mdi 4mdj 4y19 4y1a 5jlz 5lax
        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 4md5 4mdi 4mdj 4ov5 4x5w 4x5x 4y19 4y1a 5jlz 5lax 5v4m 5v4n

(-) Related Entries Specified in the PDB File

4mcy 4mcz 4md0 4md5 4mdi 4mdj