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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 :  1.65
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
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Taxid9606
    FragmentEXTRACELLULAR DOMAIN, UNP RESIDUES 26-206
    GeneHLA-DRA, HLA-DRA1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMHC CLASS II ANTIGEN DRA
 
Molecule 2 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DRB1-4 BETA CHAIN
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Taxid9606
    FragmentEXTRACELLULAR DOMAIN, UNP RESIDUES 30-219
    GeneHLA-DRB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMHC CLASS II ANTIGEN DRB1*4, DR-4, DR4
 
Molecule 3 - CITRULLINATED VIMENTIN
    ChainsC
    EngineeredYES
    FragmentRESIDUES 66-78
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsTHIS SEQUENCE IS FROM HUMAN VIMENTIN AND CONTAINS CITRULLINE AT POSITION 71
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
1CIR1Mod. Amino AcidCITRULLINE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
4PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:44 , GLU A:134 , HOH A:310 , HOH A:344 , HOH A:366 , HOH A:420 , HOH A:438BINDING SITE FOR RESIDUE EDO A 204
02AC2SOFTWAREARG A:140 , GLU A:141 , ASP A:142 , ARG A:146 , HOH A:472BINDING SITE FOR RESIDUE EDO A 205
03AC3SOFTWAREHIS A:33 , HOH A:395BINDING SITE FOR RESIDUE EDO A 206
04AC4SOFTWAREASP A:162 , HIS A:177 , HOH A:362BINDING SITE FOR RESIDUE EDO A 207
05AC5SOFTWAREVAL A:85 , PRO A:86 , HOH A:334 , HOH A:338 , HOH A:507 , HOH B:418BINDING SITE FOR RESIDUE EDO A 208
06AC6SOFTWAREASP B:76 , ARG B:166 , SER B:167 , HOH B:469 , HOH B:471 , ARG C:4BINDING SITE FOR RESIDUE EDO B 202
07AC7SOFTWAREHIS B:177 , PRO B:178 , HOH B:481BINDING SITE FOR RESIDUE EDO B 203
08AC8SOFTWARETYR A:150 , ASP B:152 , HOH B:324 , HOH B:408BINDING SITE FOR RESIDUE EDO B 204
09AC9SOFTWARESER B:42 , ASP B:43 , SER B:144 , THR B:157 , HOH B:311 , HOH B:316 , HOH B:448BINDING SITE FOR RESIDUE PGE B 205
10BC1SOFTWAREARG A:76 , ASN A:78 , LYS A:126 , HOH A:528BINDING SITE FOR MONO-SACCHARIDE NAG A 201 BOUND TO ASN A 78
11BC2SOFTWAREASN A:118 , TRP A:168 , HOH A:433 , HOH A:434 , HOH A:493 , HOH A:530 , ASP B:2 , HOH B:424BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 118 RESIDUES 202 TO 203
12BC3SOFTWAREASN B:19 , HOH B:452BINDING SITE FOR MONO-SACCHARIDE NAG B 201 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  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:15 -Pro A:16
2Thr A:113 -Pro A:114
3Tyr B:123 -Pro B:124
4Ala B:190 -Thr B:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MD5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MD5)

(-) Exons   (0, 0)

(no "Exon" information available for 4MD5)

(-) 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:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee..eee....ee...ee.....eeeeeeeee......eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4md5 A   3 EEHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFDT 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:190
                                                                                                                                                                                                                              
               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
                 4md5 B   2 DTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQRRAAVDTYCRHNYGVVESFTVQRRVYPEVTVYPAKTQPLQHHNLLVCSVNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSLTSPLTVEWRAT 191
                                    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: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
                 4md5 C   1 SAVRLrSSVPGVR  13
                                 |  10   
                                 6-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 4MD5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MD5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MD5)

(-) Gene Ontology  (80, 115)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala B:190 - Thr B:191   [ RasMol ]  
    Asn A:15 - Pro A:16   [ RasMol ]  
    Thr A:113 - Pro A:114   [ RasMol ]  
    Tyr B:123 - Pro B:124   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        2B14_HUMAN | P137601d5m 1d5x 1d5z 1d6e 1j8h 2seb 3o6f 3t0e 4is6 4mcy 4mcz 4md0 4md4 4mdi 4mdj 4y19 4y1a 5jlz 5lax
        DRA_HUMAN | P019031a6a 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 4mdi 4mdj 4ov5 4x5w 4x5x 4y19 4y1a 5jlz 5lax 5v4m 5v4n
        VIME_HUMAN | P086701gk4 1gk6 1gk7 3g1e 3klt 3s4r 3ssu 3swk 3trt 3uf1 4mcy 4mcz 4md0 4mdi 4mdj 4ypc 4yv3

(-) Related Entries Specified in the PDB File

4mcy 4mcz 4md0 4md4 4mdi 4mdj