7M8U: HLA-B*35:01

Crystal Structure of HLA-B*35:01 in complex with IPFAMQMAY, an 9-mer epitope from SARS-CoV-2 spike (S896-904). Determined by X-ray diffraction at 1.45 Å resolution. Released 23 Jun 2021.

Method: X-ray diffraction
Resolution: 1.45 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 3,590
Mol. weight: 45.24 kDa
Ligands: PO4
Released: 23 Jun 2021

Explore 7M8U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M8U contains 16 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: 12 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
α-helix	182	1
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: 4 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
α-helix	90	1
β-strand	91-94	4	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HLA class I histocompatibility antigen B, alpha chain	A	protein	277	Homo sapiens	Q546I9 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Spike protein S2 peptide	C	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7M8U_1 HLA class I histocompatibility antigen B, alpha chain (chains A)
GSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRFDSDAASPRTEPRAPWIEQEGPEYW
DRNTQIFKTNTQTYRESLRNLRGYYNQSEAGSHIIQRMYGCDLGPDGRLLRGHDQSAYDG
KDYIALNEDLSSWTAADTAAQITQRKWEAARVAEQLRAYLEGLCVEWLRRYLENGKETLQ
RADPPKTHVTHHPVSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDRT
FQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPS

Sequence of entity 2 (B), FASTA

>7M8U_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7M8U_3 Spike protein S2 peptide (chains C)
IPFAMQMAY

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2

Water and common crystallization additives (NA) are not listed.

Primary citation

SARS-CoV-2 Spike-Derived Peptides Presented by HLA Molecules. Nguyen, A.T., Szeto, C., Jayasinghe, D. et al. Biophysica (2021) 1. DOI 10.3390/biophysica1020015

Other PDB entries of the same protein (UniProt Q546I9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7SIG 1.74 Å, Crystal Structure of HLA B*3501 in complex with NPDIVIYQY, an 9-mer epitope from HIV-I

Browse structure collections

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