6BXQ: HLA-B*57:01 with an HIV peptide RKV

Crystal Structure of HLA-B*57:01 with an HIV peptide RKV. Determined by X-ray diffraction at 1.58 Å resolution. Released 28 Feb 2018.

Method: X-ray diffraction
Resolution: 1.58 Å
Organisms: Human immunodeficiency virus 1, Homo sapiens
Chains: 3
Atoms: 3,625
Mol. weight: 45.01 kDa
Released: 28 Feb 2018

Explore 6BXQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6BXQ contains 13 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 B: 11 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	9-18	10	1
α-helix	26	1
β-strand	27-34	8	1
β-strand	37-43	7	1
β-strand	52-53	2	1
α-helix	56-58	3
α-helix	63-90	28
β-strand	100-109	10	1
β-strand	115-124	10	1
β-strand	127-132	6	1
β-strand	139-141	3	1
α-helix	144-155	12
α-helix	158-165	8
α-helix	166-170	5
α-helix	171-180	10
α-helix	182-185	4
β-strand	189	1	2
α-helix	190-191	2
β-strand	192-199	8	3
β-strand	204-214	11	3
β-strand	215	1	2
β-strand	220-225	6	4
β-strand	228-229	2	4
β-strand	235-236	2	3
α-helix	237-239	3
β-strand	240-241	2	3
β-strand	247-256	10	3
α-helix	260-262	3
β-strand	263-268	6	4
β-strand	276-278	3	4

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV peptide RKV	A	protein	10	Human immunodeficiency virus 1	P04578 (AlphaFold model)
MHC class I antigen	B	protein	276	Homo sapiens	P01889 (AlphaFold model)
Beta-2-microglobulin	C	protein	100	Homo sapiens	P61771 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6BXQ_1 HIV peptide RKV (chains A)
RVKEKYQHLW

Sequence of entity 2 (B), FASTA

>6BXQ_2 MHC class I antigen (chains B)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRMAPRAPWIEQEGPEYW
DGETRNMKASAQTYRENLRIALRYYNQSEAGSHIIQVMYGCDVGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP

Sequence of entity 3 (C), FASTA

>6BXQ_3 Beta-2-microglobulin (chains C)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Primary citation

Identification of Native and Posttranslationally Modified HLA-B*57:01-Restricted HIV Envelope Derived Epitopes Using Immunoproteomics. Ramarathinam, S.H., Gras, S., Alcantara, S. et al. Proteomics (2018) 18:e1700253-e1700253. DOI 10.1002/pmic.201700253 · PubMed

Other PDB entries of the same protein (UniProt P04578 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8F3A 1.2 Å, HIV-1 gp41 coiled-coil pocket IQN17
6UCF 1.29 Å, N123-VRC34_pI4 HIV neutralizing antibody in complex with HIV fusion peptide residue…
6PSA 1.3 Å, PIE12 D-peptide against HIV entry (in complex with IQN17 Q577R resistance mutant)
6UCE 1.38 Å, N123-VRC34_pI3 HIV neutralizing antibody in complex with HIV fusion peptide residue…
9ARN 1.41 Å, Structure and interactions of HIV-1 gp41 CHR-NHR reverse hairpin constructs reveal…
1DF4 1.45 Å, Interactions between HIV-1 GP41 core and detergents and their implications for membrane…
6BXP 1.45 Å, Crystal Structure of HLA-B*57:01 with a modified HIV peptide RKV-Kyn
7EKB 1.45 Å, Crystal structure of 4E10 modified with pyrene acetamide
5X08 1.49 Å, Crystal structure of broadly neutralizing anti-HIV-1 antibody 4E10, mutant Npro, with…
6JQK 1.5 Å, Structure of C34M/N36
5TKK 1.55 Å, Structure of mouse vaccination-elicited HIV neutralizing antibody vFP5.01 in complex…
6PDR 1.55 Å, Vaccine-elicited murine FP-targeting antibody vFP25.18 in complex with HIV fusion…

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