7KGS: HLA-A*0201

Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N138-146. Determined by X-ray diffraction at 1.58 Å resolution. Released 20 Jan 2021.

Method: X-ray diffraction
Resolution: 1.58 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 3
Atoms: 3,783
Mol. weight: 45.2 kDa
Ligands: CD
Released: 20 Jan 2021

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

Secondary structure: helices and β-sheets

7KGS contains 12 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: 10 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	152-158	7
α-helix	159-163	5
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	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	222-224	3	4
β-strand	228-230	3	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: 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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A	protein	278	Homo sapiens	Q861F7 (AlphaFold model)
Beta-2-microglobulin	B	protein	99	Homo sapiens	P61769 (AlphaFold model)
Nucleoprotein	C	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7KGS_1 MHC class I antigen (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWVAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSS

Sequence of entity 2 (B), FASTA

>7KGS_2 Beta-2-microglobulin (chains B)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7KGS_3 Nucleoprotein (chains C)
ALNTPKDHI

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	2

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

Primary citation

The presentation of SARS-CoV-2 peptides by the common HLA-A*02:01 molecule. Szeto, C., Chatzileontiadou, D.S.M., Nguyen, A.T. et al. iScience (2021) 24:102096-102096. DOI 10.1016/j.isci.2021.102096 · PubMed

Other PDB entries of the same protein (UniProt Q861F7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KGQ 1.34 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N222-230
7KGP 1.4 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N316-324
7KGR 1.55 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N159-167
7T5M 1.67 Å, Structure of HLA-A*02:01-FLPTPEELGLLGPPRPQVLA complex
7PDW 1.82 Å, Crystal structure of parent TCR (728) complexed to HLA-A*02:01 presenting MAGE-A10 9-mer…
7KGT 1.9 Å, Crystal Structure of HLA-A*0201 in complex with SARS-CoV-2 N226-234
7SIS 1.9 Å, SARS-CoV-2 Spike-derived peptide S976-984 (VLNDILSRL) presented by HLA-A*02:01
7PBC 2.04 Å, Crystal structure of engineered TCR (796) complexed to HLA-A*02:01 presenting MAGE-A10…
7KGO 2.15 Å, Crystal Structure of HLA-A*0201in complex with SARS-CoV-2 N351-359
8ES8 2.65 Å, CryoEM structure of PN45545 TCR-CD3 in complex with HLA-A2 MAGEA4 (230-239)
8FJA 3.0 Å, CryoEM structure of HLA-A2 MAGEA4 (230-239) in complex with REGN6972 Fab
8FJB 3.06 Å, CryoEM structure of HLA-A2 MAGEA4 (286-294) in complex with H2aM31345N Fab

Browse structure collections

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