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(-) Description

Title :  IMMUNE COMPLEX
 
Authors :  D. X. Beringer, J. P. Vivian, H. H. Reid, J. Rossjohn
Date :  07 Feb 15  (Deposition) - 23 Sep 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Tcr Mhc, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. X. Beringer, F. S. Kleijwegt, F. Wiede, A. R. Van Der Slik, K. L. Loh J. Petersen, N. L. Dudek, G. Duinkerken, S. Laban, A. Joosten, J. P. Vivian, Z. Chen, A. P. Uldrich, D. I. Godfrey, J. Mccluskey, D. A. Price, K. J. Radford, A. W. Purcell, T. Nikolic, H. H. Reid, T. Tiganis, B. O. Roep, J. Rossjohn
T Cell Receptor Reversed Polarity Recognition Of A Self-Antigen Major Histocompatibility Complex.
Nat. Immunol. V. 16 1153 2015
PubMed-ID: 26437244  |  Reference-DOI: 10.1038/NI.3271

(-) Compounds

Molecule 1 - HLA CLASS II HISTOCOMPATIBILITY ANTIGEN, DR ALPHA CHAIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293S
    Expression System Taxid: 9606
    Fragment: 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 Cell Line: HEK293S
    Expression System Taxid: 9606
    Fragment: UNP RESIDUES 30-219
    Gene: HLA-DRB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MHC CLASS II ANTIGEN DRB1*4,DR4
 
Molecule 3 - INSULIN
    Chains: C
    Engineered: YES
    Fragment: UNP RESIDUES 75-90
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 4 - FS17_ALPHA
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 5 - FS17_BETA
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:118 , TRP A:168 , GLY B:1binding site for Poly-Saccharide residues NAG A 600 through NAG A 601 bound to ASN A 118

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1A:107 -A:163
2B:15 -B:79
3B:117 -B:173
4D:23 -D:104
5D:153 -D:203
6D:178 -E:182
7E:23 -E:104
8E:156 -E:221

(-) Cis Peptide Bonds  (16, 16)

Asymmetric/Biological Unit
No.Residues
1Asn A:15 -Pro A:16
2Thr A:113 -Pro A:114
3Tyr B:123 -Pro B:124
4Val B:164 -Pro B:165
5Ser B:167 -Gly B:168
6Val D:92 -Pro D:93
7Ala D:110 -Gly D:111
8Gly D:111 -Gly D:112
9Gly D:112 -Thr D:113
10Tyr D:115 -Gly D:116
11Ser D:148 -Asp D:149
12Phe D:201 -Ala D:202
13Thr E:7 -Pro E:8
14Gly E:58 -Glu E:59
15Glu E:59 -Gly E:60
16Phe E:162 -Pro E:163

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y1A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y1A)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y1A)

(-) 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:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee...eeeeeeee..eeeeeee....eeee.hhhhhh.ee.hhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.........eeeeeeeeee.....eeeeee.........ee...ee.....eeeeeeeee......eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y1a A   4 EHVIIQAEFYLNPDQSGEFMFDFDGDEIFHVDMAKKETVWRLEEFGRFASFEAQGALANIAVDKANLEIMTKRSNYTPITNVPPEVTVLTNSPVELREPNVLICFIDKFTPPVVNVTWLRNGKPVTTGVSETVFLPREDHLFRKFHYLPFLPSTEDVYDCRVEHWGLDEPLLKHWEFD 181
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173        


Chain B from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeeee....eeeeeeeeee..eeeeeee.....eee.hhhhhhhhhhhhhh.hhhhhh.hhhhhhhhhhhhhhhhhhh......eeeeee..eeeeeeeee.....eeeeee..ee....ee....ee.....eeeeeeee........eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y1a B   0 SGDTRPRFLEQVKHECHFFNGTERVRFLDRYFYHQEEYVRFDSDVGEYRAVTELGRPDAEYWNSQKDLLEQKRAAVDTYCRHNYGVGESFTVQRRVYPEVTVYPANLLVCSVNGFYPGSIEVRWFRNGQEEKTGVVSTGLIQNGDWTFQTLVMLETVPRSGEVYTCQVEHPSLTSPLTVEWRAT 191
                                     9        19        29        39        49        59        69        79        89        99    || 117       127       137       147       157       167       177       187    
                                                                                                                                  104|                                                                              
                                                                                                                                   113                                                                              


Chain C from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .ee........... Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 4y1a C  -2 LQPLALEGSLQKRG  11
                                     7    


Chain D from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeeee....eeeeeee....eeeeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeeeee..........ee...eeeeee........eeeeee.......eeeeee...............eee...eeeee....eeeeeeeeee.......hhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y1a D   1 MQQVKQNSPSLSVQEGRISILNCDYTNSMFDYFLWYKKYPAEGPTFLISISSIKDKNEDGRFTVFLNKSAKHLSLHIVPSQPGDSAVYFCAASSSAGGTSYGKLTFGQGTILTVHPNIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFP 219
                                    10        20        36        46        56  ||    74        84        94       104       114       124       134       144       154       164       174       184       194       204       214     
                                                       29|                     59|   68|                                                                                                                                                 
                                                        36                      63    74                                                                                                                                                 


Chain E from PDB  Type:PROTEIN  Length:240
                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee..eeeee....eeeeee......eeeeeeee...eeeeeeee...............eee.....eeeeee...hhhhheeeeeeee.......ee...eeeeee.........eeeee..hhhhhhhh.eeeeeeeeeee....eeeeeee..eee...eee....ee.........eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4y1a E   2 AGVTQTPKFRVLKTGQSMTLLCAQDMNHEYMYWYRQDPGMGLRLIHYSVGEGTTAKGEVPDGYNVSRLKKQNFLLGLESAAPSQTSVYFCASRPRDPVTQYFGPGTRLTVLEDLKNVFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAWGRA 254
                                    11        21       |38        48        58 ||     72|      |84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
                                                      29|                     60|     72|     81|                                                                                                                                                                           
                                                       37                      65      74      83
   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 4Y1A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y1A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y1A)

(-) Gene Ontology  (124, 157)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala D:110 - Gly D:111   [ RasMol ]  
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  4y1a
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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 4md4 4md5 4mdi 4mdj 4y19 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 4md4 4md5 4mdi 4mdj 4ov5 4x5w 4x5x 4y19 5jlz 5lax 5v4m 5v4n
        INS_HUMAN | P01308: 1a7f 1ai0 1aiy 1b9e 1ben 1efe 1ev3 1ev6 1evr 1fu2 1fub 1g7a 1g7b 1guj 1hiq 1his 1hit 1hls 1htv 1hui 1iog 1ioh 1j73 1jca 1jco 1jk8 1k3m 1kmf 1lkq 1lph 1mhi 1mhj 1mso 1os3 1os4 1q4v 1qiy 1qiz 1qj0 1rwe 1sf1 1sjt 1sju 1t0c 1t1k 1t1p 1t1q 1trz 1tyl 1tym 1uz9 1vkt 1w8p 1xda 1xgl 1xw7 1zeg 1zeh 1znj 2aiy 2c8q 2c8r 2ceu 2g54 2g56 2h67 2hh4 2hho 2hiu 2jmn 2jum 2juu 2juv 2jv1 2jzq 2k91 2k9r 2kjj 2kju 2kqp 2kqq 2kxk 2l1y 2l1z 2lgb 2lwz 2m1d 2m1e 2m2m 2m2n 2m2o 2m2p 2mli 2mpg 2mpi 2mvc 2mvd 2n2v 2n2w 2n2x 2oly 2olz 2om0 2om1 2omg 2omh 2omi 2omq 2qiu 2r34 2r35 2r36 2rn5 2vjz 2vk0 2w44 2wby 2wc0 2wru 2wrv 2wrw 2wrx 2ws0 2ws1 2ws4 2ws6 2ws7 3aiy 3bxq 3e7y 3e7z 3exx 3fq9 3hyd 3i3z 3i40 3ilg 3inc 3ir0 3jsd 3kq6 3p2x 3p33 3q6e 3rov 3tt8 3u4n 3utq 3uts 3utt 3v19 3v1g 3w11 3w12 3w13 3w7y 3w7z 3w80 3zi3 3zqr 3zs2 3zu1 4aiy 4ajx 4ajz 4ak0 4akj 4cxl 4cxn 4cy7 4efx 4eww 4ewx 4ewz 4ex0 4ex1 4exx 4ey1 4ey9 4eyd 4eyn 4eyp 4f0n 4f0o 4f1a 4f1b 4f1c 4f1d 4f1f 4f1g 4f4t 4f4v 4f51 4f8f 4fg3 4fka 4gbc 4gbi 4gbk 4gbl 4gbn 4iuz 4iyd 4iyf 4nib 4oga 4p65 4q5z 4rxw 4une 4ung 4unh 4wdi 4xc4 4y19 4z76 4z77 4z78 5aiy 5boq 5bpo 5bqq 5bts 5c0d 5cjo 5cny 5co2 5co6 5co9 5e7w 5ems 5en9 5ena 5hpr 5hpu 5hqi 5hrq 5hyj 5mam 5mt3 5mt9 5udp

(-) Related Entries Specified in the PDB File

4y19