7R7W: MHC class I antigen

Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9 S3T variant. Determined by X-ray diffraction at 1.17 Å resolution. Released 29 Jun 2022.

Method: X-ray diffraction
Resolution: 1.17 Å
Organisms: Homo sapiens, HIV-1 06TG.HT008
Chains: 3
Atoms: 3,895
Mol. weight: 45.24 kDa
Released: 29 Jun 2022

Explore 7R7W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R7W contains 14 α-helices and 30 β-strands across 2 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: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	57-84	28
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-126	6	1
β-strand	133-135	3	1
α-helix	138-149	12
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
α-helix	225-227	3
β-strand	229-230	2	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	257-262	6	4
β-strand	270-272	3	4

Chain B: 3 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
α-helix	46	1
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	78-83	6	7
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	278	Homo sapiens	S6BVK3 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Gln-ala-thr-gln-glu-val-lys-asn-trp	C	protein	9	HIV-1 06TG.HT008	O91080

Sequence of entity 1 (A), FASTA

>7R7W_1 MHC class I antigen (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRENLRIALRYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPHH

Sequence of entity 2 (B), FASTA

>7R7W_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7R7W_3 GLN-ALA-THR-GLN-GLU-VAL-LYS-ASN-TRP (chains C)
QATQEVKNW

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:

7R7V 1.6 Å, Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9
7R80 2.9 Å, Crystal structure of C3 TCR complex with QW9-bound HLA-B*5301

Browse structure collections

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