7F4W: MHC class I antigen

Complex structure of HLA2402 with recognizing SARS-CoV-2 epitope pep4. Determined by X-ray diffraction at 2.9 Å resolution. Released 25 Aug 2021.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 6
Atoms: 6,388
Mol. weight: 97.59 kDa
Released: 25 Aug 2021

Explore 7F4W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7F4W contains 20 α-helices and 60 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: 9 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	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	138-148	11
α-helix	152-160	9
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-192	7	3
β-strand	200-208	9	3
β-strand	209	1	2
β-strand	214-219	6	4
β-strand	222-223	2	4
β-strand	228-230	3	3
α-helix	231-233	3
β-strand	234-235	2	3
β-strand	241-248	8	3
α-helix	254-256	3
β-strand	257-262	6	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	52-54	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

Chain C: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	8
α-helix	20	1
β-strand	21-28	8	8
β-strand	31-37	7	8
β-strand	46-47	2	8
α-helix	50-52	3
α-helix	57-85	29
β-strand	94-103	10	8
β-strand	109-118	10	8
β-strand	121-126	6	8
β-strand	133-135	3	8
α-helix	140-148	9
α-helix	152-161	10
α-helix	163-174	12
β-strand	183	1	9
α-helix	184-185	2
β-strand	186-193	8	10
β-strand	198-206	9	10
β-strand	209	1	9
β-strand	214-219	6	11
β-strand	222-223	2	11
β-strand	228-230	3	10
α-helix	231-233	3
β-strand	234-235	2	10
β-strand	241-250	10	10
β-strand	257-262	6	11
β-strand	270-272	3	11

Chain D: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	12
α-helix	4-5	2
β-strand	6-11	6	13
β-strand	21-30	10	13
β-strand	31	1	12
β-strand	36-41	6	14
β-strand	44-45	2	14
β-strand	50-51	2	13
β-strand	55-56	2	13
β-strand	62-70	9	13
β-strand	78-83	6	14
β-strand	91-94	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, C	protein	308	Homo sapiens	D9UAY1 (AlphaFold model)
Beta-2-microglobulin	B, D	protein	102	Homo sapiens	P61769 (AlphaFold model)
SARS-CoV-2 T-cell Epitope pep4	E, F	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>7F4W_1 MHC class I antigen (chains A, C)
MNSVDGSHSMRYFSTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQE
GPEYWDEETGKVKAHSQTDRENLRIALRYYNQSEAGSHTLQMMFGCDVGSDGRFLRGYHQ
YAYDGKDYIALKEDLRSWTAADMAAQITKRKWEAAHVAEQQRAYLEGTCVDGLRRYLENG
KETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRP
AGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEPGSGLNDIFEAQKIEWHAAA
LEHHHHHH

Sequence of entity 2 (B, D), FASTA

>7F4W_2 Beta-2-microglobulin (chains B, D)
VDMIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFS
KDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (E, F), FASTA

>7F4W_3 SARS-CoV-2 T-cell Epitope pep4 (chains E, F)
NYNYLYRLF

Primary citation

Profiling CD8 + T cell epitopes of COVID-19 convalescents reveals reduced cellular immune responses to SARS-CoV-2 variants. Zhang, H., Deng, S., Ren, L. et al. Cell Rep (2021) 36:109708-109708. DOI 10.1016/j.celrep.2021.109708 · PubMed

Other PDB entries of the same protein (UniProt D9UAY1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8ISN 2.48 Å, HLA-A24 in complex with modified 9mer WT1 peptide

Browse structure collections

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