5IVX: B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex

Crystal Structure of B4.2.3 T-Cell Receptor and H2-Dd P18-I10 Complex. Determined by X-ray diffraction at 2.1 Å resolution. Released 29 Mar 2017.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Mus musculus, Homo sapiens
Chains: 5
Atoms: 7,026
Mol. weight: 93.88 kDa
Released: 29 Mar 2017

Explore 5IVX in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IVX contains 24 α-helices and 76 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-12	11	1
α-helix	20	1
β-strand	21-28	8	1
β-strand	31-37	7	1
β-strand	46-47	2	1
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-104	11	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-150	13
α-helix	153-158	6
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	199-208	10	3
β-strand	209	1	2
β-strand	214-217	4	4
β-strand	228-230	3	3
β-strand	234-235	2	3
β-strand	241-249	9	3
α-helix	253-255	3
β-strand	259-262	4	4
β-strand	270-272	3	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
α-helix	4-5	2
β-strand	6-11	6	6
β-strand	21-30	10	6
β-strand	31	1	5
β-strand	36-41	6	7
β-strand	44-45	2	7
β-strand	50-51	2	6
α-helix	52-53	2
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	78-83	6	7
β-strand	91-94	4	7

Chain E: 5 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	8
β-strand	11-15	5	9
α-helix	19	1
β-strand	20-26	7	8
β-strand	33-39	7	9
β-strand	46-52	7	9
β-strand	57-60	4	8
β-strand	63-68	6	8
β-strand	73-78	6	8
α-helix	83-85	3
β-strand	87-91	5	9
β-strand	92-93	2	10
β-strand	94	1	9
α-helix	102-103	2
β-strand	104-105	2	10
α-helix	106	1
β-strand	109-114	6	9
β-strand	123-127	5	11
β-strand	128	1	12
β-strand	137-141	5	11
β-strand	158-159	2	11
α-helix	160-162	3
β-strand	165-167	3	13
β-strand	172-174	3	13
β-strand	176-180	5	11

Chain F: 7 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
β-strand	9-13	5	15
β-strand	18-20	3	16
β-strand	21-24	4	14
β-strand	30-36	7	15
β-strand	42-50	9	15
β-strand	53-56	4	15
β-strand	64-66	3	16
β-strand	72	1	14
β-strand	74-77	4	16
α-helix	82-84	3
β-strand	86-93	8	15
α-helix	98-99	2
β-strand	100-101	2	15
β-strand	105-110	6	15
α-helix	113-115	3
β-strand	117	1	17
α-helix	118-119	2
β-strand	120-124	5	18
β-strand	125	1	12
α-helix	126-127	2
α-helix	128-134	7
β-strand	136-146	11	18
β-strand	147	1	17
β-strand	151-157	7	19
β-strand	160-162	3	19
β-strand	166-168	3	18
β-strand	173-174	2	18
β-strand	180-189	10	18
α-helix	190-193	4
β-strand	199-206	8	19
β-strand	209	1	20
β-strand	223	1	20
β-strand	225-232	8	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
H-2 class I histocompatibility antigen, D-D alpha chain	A	protein	277	Mus musculus	P01900 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Mus musculus	P01887 (AlphaFold model)
T-cell receptor alpha chain	E	protein	194	Mus musculus
T-cell receptor beta chain	F	protein	234	Mus musculus
P18-I10	P	protein	10	Homo sapiens	P04578 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5IVX_1 H-2 class I histocompatibility antigen, D-D alpha chain (chains A)
MSHSLRYFVTAVSRPGFGEPRYMEVGYVDNTEFVRFDSDAENPRYEPRARWIEQEGPEYW
ERETRRAKGNEQSFRVDLRTALRYYNQSAGGSHTLQWMAGCDVESDGRLLRGYWQFAYDG
CDYIALNEDLKTWTAADMAAQITRRKWEQAGAAERDRAYLEGECVEWLRRYLKNGNATLL
RTDPPKAHVTHHRRPEGDVTLRCWALGFYPADITLTWQLNGEELTQEMELVETRPAGDGT
FQKWASVVVPLGKEQKYTCHVEHEGLPEPLTLRWGKE

Sequence of entity 2 (B), FASTA

>5IVX_2 Beta-2-microglobulin (chains B)
MIQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKD
WSFYILAHTEFTPTETDTYACRVKHASMAEPKTVYWDRDM

Sequence of entity 3 (E), FASTA

>5IVX_3 T-CELL RECEPTOR ALPHA CHAIN (chains E)
QQVRQSPQSLTVWEGETAILNCSYENSAFDYFPWYQQFPGEGPALLISILSVSNKKEDGR
FTIFFNKREKKLSLHIADSQPGDSATYFCAASASFGDNSKLIWGLGTSLVVNPNIQNPEP
AVYQLKDPRSQDSTLCLFTDFDSQINVPKTMESGTFITDKCVLDMKAMDSKSNGAIAWSN
QTSFTCQDIFKETN

Sequence of entity 4 (F), FASTA

>5IVX_4 T-CELL RECEPTOR BETA CHAIN (chains F)
MKVTQMPRYLIKRMGENVLLECGQDMSHETMYWYRQDPGLGLQLIYISYDVDSNSEGDIP
KGYRVSRKKREHFSLILDSAKTNQTSVYFCASSLGHTEVFFGKGTRLTVVEDLRNVTPPK
VSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVCTDPQAYKESNYSY
ALSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGR

Sequence of entity 5 (P), FASTA

>5IVX_5 P18-I10 (chains P)
RGPGRAFVTI

Primary citation

An allosteric site in the T-cell receptor C beta domain plays a critical signalling role. Natarajan, K., McShan, A.C., Jiang, J. et al. Nat Commun (2017) 8:15260-15260. DOI 10.1038/ncomms15260 · PubMed

Other PDB entries of the same protein (UniProt P01900 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5WEU 1.58 Å, Crystal Structure of H2-Dd with disulfide-linked 10mer peptide
3ECB 1.7 Å, Crystal structure of mouse H-2Dd in complex with peptide P18-I10 derived from human…
8FHU 1.8 Å, Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by…
5T7G 1.96 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
3E6H 2.1 Å, MHC CLASS I H-2Dd heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…
8FHL 2.19 Å, Structure of pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented…
1QO3 2.3 Å, Complex between NK cell receptor Ly49A and its MHC class I ligand H-2Dd
8D5F 2.31 Å, The complex of Gtf2b neoantigen TGAARFDEF Presented by H2-Dd
5KD7 2.35 Å, Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a…
6NPR 2.37 Å, Crystal structure of H-2Dd with C84-C139 disulfide in complex with gp120 derived peptide…
1BII 2.4 Å, The crystal structure of H-2DD MHC class I in complex with the HIV-1 derived peptide…
3E6F 2.41 Å, MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide,…

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