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(-) Description

Title :  CRYSTAL STRUCTURE OF B4.2.3 T-CELL RECEPTOR AND H2-DD P18-I10 COMPLEX
 
Authors :  K. Natarajan, J. Jiang, D. Margulies
Date :  21 Mar 16  (Deposition) - 29 Mar 17  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,E,F,P
Keywords :  Major Histompatibility Complex Class I, Mhc-I, H2-Dd, H-2Dd, T-Cell Receptor, Tcr, B4. 2. 3, B423, Immune Response, Viral Immunoevasion, Immune System, Human Immunodeficiency Virus, Molecular Recognition (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Natarajan, A. C. Mcshan, J. Jiang, V. K. Kumirov, R. Wang, H. Zhao, P. Schuck, M. E. Tilahun, L. F. Boyd, J. Ying, A. Bax, D. H. Margulies, N. G. Sgourakis
An Allosteric Site In The T-Cell Receptor C Beta Domain Plays A Critical Signalling Role.
Nat Commun V. 8 15260 2017
PubMed-ID: 28508865  |  Reference-DOI: 10.1038/NCOMMS15260

(-) Compounds

Molecule 1 - H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, D-D ALPHA CHAIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21-B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: H2-D1
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: H-2D(D)
 
Molecule 2 - BETA-2-MICROGLOBULIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: B2M
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 3 - T-CELL RECEPTOR ALPHA CHAIN
    Cell: T LYMPHOCYTE
    Cell Line: B4.2.3 T CELL HYBRIDOMA
    Chains: E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TCRAV2S6J38
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 4 - T-CELL RECEPTOR BETA CHAIN
    Chains: F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 5 - P18-I10
    Chains: P
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: THE PEPTIDE IS CHEMICALLY SYNTHESIZED. FOUND NATURALLY IN HUMAN IMMUNODEFICIENCY VIRUS ENVELOPE SOURCE 26 GLYCOPROTEIN GP120.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABEFP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:151 , GLU A:154 , ARG A:155 , HOH A:485 , HOH E:326binding site for residue EDO A 301
2AC2SOFTWAREARG A:83 , HOH A:432 , GLU F:71binding site for residue EDO A 302
3AC3SOFTWAREVAL A:12 , HIS B:34 , HOH B:244binding site for residue EDO B 101
4AC4SOFTWAREPHE E:66 , LEU E:74 , SER E:75 , HOH E:334binding site for residue EDO E 201

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:101 -A:164
2A:203 -A:259
3B:25 -B:80
4E:138 -E:188
5E:163 -F:167
6F:22 -F:90
7F:141 -F:202

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Tyr A:209 -Pro A:210
2His B:31 -Pro B:32
3Ser E:8 -Pro E:9
4Met F:6 -Pro F:7
5Phe F:147 -Pro F:148

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IVX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IVX)

(-) Exons   (0, 0)

(no "Exon" information available for 5IVX)

(-) 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:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee........eeeeeeee..eeeeeee........ee.hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeeee....eeeeeeeeee..eeeeee......eee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeee.....eeeeeeeeee.....eeee..........eee...ee.....eeeeeeeee..hhhhh..eeee.......eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ivx A   1 MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYWERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDGCDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLLRTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGTFQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRW 274
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270    


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee.........eeeeeeeeee.....eeeeee..ee....ee...ee.....eeeeeeeee.......eeeeee.......eeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5ivx B   1 IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM  99
                                    10        20        30        40        50        60        70        80        90         


Chain E from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee......eeeeeee......eeeeeee....eeee..eeeeee....eeeeee...hhhhheeeeeee..........ee...eeeeee........eeeee.........eeeee................ee...eeeee....eeeeeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ivx E   3 QQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSNKKEDGRFTIFFNKREKKLSLHIADSQPGDSATYFCAASASFGDNSKLIWGLGTSLVVNPNIQNPEPAVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMKAMDSKSNGAIAWSNQTSFTCQDIFKETN 196
                                    12        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:234
                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee..eeeee....eeeeeee.....eeeeeee.....eeeeeeeee..eeee.......eee.......eeee...hhhhheeeeeeee......ee...eeeeee.hhhhh...eeeee..hhhhhhhhheeeeeeeeeee....eeeeeee..eee...eee....ee.....eeeeeeeeeehhhhh....eeeeeeee..................eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5ivx F   1 MKVTQMPRYLIKRMGENVLLECGQDMSHETMYWYRQDPGLGLQLIYISYDVDSNSEGDIPKGYRVSRKKREHFSLILDSAKTNQTSVYFCASSLGHTEVFFGKGTRLTVVEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKESNYSYALSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGR 234
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    


Chain P 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
                 5ivx P   1 RGPGRAFVTI  10
                                    10
   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 5IVX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IVX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IVX)

(-) Gene Ontology  (87, 104)

Asymmetric/Biological Unit(hide GO term definitions)

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  HA12_MOUSE | P01900
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 Related Entries

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

UniProtKB/Swiss-Prot
        B2MG_MOUSE | P01887: 1bii 1bqh 1bz9 1cd1 1ddh 1ffn 1ffo 1ffp 1fg2 1fo0 1fzj 1fzk 1fzm 1fzo 1g6r 1g7p 1g7q 1hoc 1inq 1jpf 1jpg 1juf 1k8d 1kbg 1kj2 1kj3 1kpu 1kpv 1l6q 1ld9 1ldp 1leg 1lek 1lk2 1mhc 1mwa 1n3n 1n59 1n5a 1nam 1nan 1nez 1osz 1p1z 1p4l 1pqz 1qo3 1rjy 1rjz 1rk0 1rk1 1s7q 1s7r 1s7s 1s7t 1s7u 1s7v 1s7w 1s7x 1t0m 1t0n 1u58 1vac 1vad 1wbx 1wby 1wbz 1yn6 1yn7 1z5l 1zhb 1zhn 1zt1 1zt7 2akr 2ckb 2clv 2clz 2fik 2fo4 2fwo 2gaz 2mha 2ol3 2q7y 2qri 2qrs 2qrt 2vaa 2vab 2ve6 2zok 2zol 2zsv 2zsw 3arb 3ard 3are 3arf 3arg 3au1 3buy 3c8k 3cc5 3cch 3ch1 3cpl 3cvh 3dmm 3e6f 3e6h 3ecb 3fol 3fom 3fon 3ftg 3g08 3gml 3gmm 3gmn 3gmo 3gmp 3gmq 3gmr 3he6 3he7 3ilp 3ilq 3l3h 3ma7 3nwm 3o8x 3o9w 3p4m 3p4n 3p4o 3p9l 3p9m 3pab 3pqy 3pwu 3qi9 3quk 3qul 3qux 3quy 3quz 3rgv 3rol 3roo 3rtq 3rug 3rzc 3scm 3sda 3sdc 3sdd 3t1f 3ta3 3tbs 3tbt 3tbv 3tbw 3tby 3tn0 3to4 3tvm 3ubx 3vj6 3ws3 3ws6 4apq 4ei5 4elm 4hs3 4huu 4huv 4huw 4hux 4hv8 4iho 4irj 4irs 4l8b 4l8c 4l8d 4mng 4mq7 4mx7 4nsk 4pg2 4pg9 4pgb 4pgc 4pgd 4pge 4pv8 4pv9 4y16 4y2d 4y4f 4y4h 4y4k 4zak 4zus 4zut 4zuu 4zuv 4zuw 5e8n 5e8o 5e8p 5efi 5fkp 5j6g 5j6h 5jwd 5jwe 5sws 5swz
        ENV_HV1H2 | P04578: 1aik 1df4 1df5 1dlb 1g9m 1gc1 1gzl 1k33 1k34 1mzi 1opn 1opt 1opw 1rzj 2cmr 2me1 2mg1 2mg2 2mg3 2ny7 2pv6 2x7r 2xra 2zzo 3d0v 3dnl 3dnn 3dno 3dro 3idx 3idy 3j70 3tyg 3vie 4jpj 4jpk 4ydv 4zto 5bn0 5c0r 5c0s 5cil 5cin 5cmu 5cmz 5cn0 5dd0 5ghw 5h0n 5hfl 5hm1 5ka5 5ka6 5x08
        HA12_MOUSE | P01900: 1bii 1ddh 1qo3 3dmm 3e6f 3e6h 3ecb

(-) Related Entries Specified in the PDB File

5iw1