7R80: C3 TCR complex with QW9-bound HLA-B*5301

Crystal structure of C3 TCR complex with QW9-bound HLA-B*5301. Determined by X-ray diffraction at 2.9 Å resolution. Released 29 Jun 2022.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, HIV-1 06TG.HT008
Chains: 5
Atoms: 6,410
Mol. weight: 95.25 kDa
Released: 29 Jun 2022

Explore 7R80 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R80 contains 19 α-helices and 71 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: 4 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	8
β-strand	10-14	5	9
β-strand	19-24	6	8
β-strand	32-39	8	9
β-strand	43-51	9	9
β-strand	56-59	4	8
β-strand	62-67	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	87-93	7	9
β-strand	100-102	3	9
β-strand	106-111	6	9
α-helix	112-113	2
β-strand	120-123	4	10
β-strand	134-138	5	10
α-helix	149-151	3
β-strand	155-156	2	10
β-strand	160-164	5	10
β-strand	169-173	5	10
β-strand	176-177	2	10
α-helix	198-200	3

Chain B: 6 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	10-14	5	12
β-strand	19-21	3	13
β-strand	22-24	3	11
β-strand	31-38	8	12
β-strand	42-51	10	12
β-strand	54-57	4	12
β-strand	65-66	2	13
β-strand	73	1	11
β-strand	76-78	3	13
α-helix	83-85	3
β-strand	87-94	8	12
β-strand	104-105	2	12
β-strand	109-114	6	12
α-helix	117-119	3
β-strand	121	1	14
β-strand	124-128	5	15
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	15
β-strand	151	1	14
β-strand	155-161	7	16
β-strand	164-165	2	16
β-strand	170-172	3	15
β-strand	177-178	2	15
β-strand	188-197	10	15
α-helix	198-202	5
β-strand	207-214	8	16
β-strand	217	1	17
α-helix	228-229	2
β-strand	231	1	17
β-strand	233-240	8	16

Chain C: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-14	12	1
β-strand	18-28	11	1
β-strand	31-37	7	1
α-helix	45	1
β-strand	46-47	2	1
α-helix	51-54	4
α-helix	57-85	29
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-122	2	1
β-strand	126	1	2
β-strand	133	1	2
α-helix	138-149	12
α-helix	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	189-192	4	3
β-strand	199-206	8	3
β-strand	213-218	6	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-249	9	3
β-strand	258-263	6	4
β-strand	270	1	4

Chain D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	5
β-strand	6-9	4	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	52-54	3
β-strand	55-56	2	6
β-strand	62-70	9	6
β-strand	79-83	5	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	C	protein	278	Homo sapiens	S6BVK3 (AlphaFold model)
Beta-2-microglobulin	D	protein	100	Homo sapiens	P61769 (AlphaFold model)
Gln-ala-ser-gln-glu-val-lys-asn-trp	E	protein	9	HIV-1 06TG.HT008	P04585 (AlphaFold model)
Alpha chain of C3 TCR	A	protein	208	Homo sapiens
Beta Chain of C3 TCR	B	protein	246	Homo sapiens

Sequence of entity 1 (C), FASTA

>7R80_1 MHC class I antigen (chains C)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRENLRIALRYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPHH

Sequence of entity 2 (D), FASTA

>7R80_2 Beta-2-microglobulin (chains D)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E), FASTA

>7R80_3 GLN-ALA-SER-GLN-GLU-VAL-LYS-ASN-TRP (chains E)
QASQEVKNW

Sequence of entity 4 (A), FASTA

>7R80_4 Alpha chain of C3 TCR (chains A)
MKQEVTQIPAALSVPEGENLVLNCSFTDSAIYNLQWFRQDPGKGLTSLLLIQSSQREQTS
GRLNASLDKSSGRSTLYIAASQPGDSATYLCAQLNQAGTALIFGKGTTLSVSSNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESSS

Sequence of entity 5 (B), FASTA

>7R80_5 Beta Chain of C3 TCR (chains B)
MNAGVTQTPKFQVLKTGQSMTLQCAQDMNHEYMSWYRQDPGMGLRLIHYSVGAGITDQGE
VPNGYNVSRSTTEDFPLRLLSAAPSQTSVYFCASSYGTGINYGYTFGSGTRLTVVEDLNK
VFPPEVAVFEPSEAEISHTQKATLVCLATGFFPDHVELSWWVNGKEVHSGVCTDPQPLKE
QPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEA
WGRADS

Primary citation

Molecular basis of differential HLA class I-restricted T cell recognition of a highly networked HIV peptide. Li, X., Singh, N.K., Collins, D.R. et al. Nat Commun (2023) 14:2929-2929. DOI 10.1038/s41467-023-38573-8 · PubMed

Other PDB entries of the same protein (UniProt S6BVK3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7R7W 1.17 Å, Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9 S3T variant
7R7V 1.6 Å, Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9

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