7N1E: MHC class I antigen, A-2 alpha chain

SARS-CoV-2 RLQ peptide-specific TCR pRLQ3 binds to RLQ-HLA-A2. Determined by X-ray diffraction at 2.3 Å resolution. Released 28 Jul 2021.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, Severe acute respiratory syndrome coronavirus 2
Chains: 5
Atoms: 6,884
Mol. weight: 95.09 kDa
Released: 28 Jul 2021

Explore 7N1E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7N1E contains 29 α-helices and 75 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: 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	50-54	5
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	138-150	13
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
α-helix	176-179	4
β-strand	183	1	2
α-helix	184-185	2
β-strand	186-193	8	3
β-strand	199-208	10	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	241-249	9	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

Chain D: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	8
β-strand	9-13	5	9
β-strand	18-20	3	10
β-strand	23-25	3	8
β-strand	30-37	8	9
β-strand	44-48	5	9
α-helix	49-51	3
β-strand	55	1	11
β-strand	58	1	11
β-strand	59-60	2	10
β-strand	63	1	8
β-strand	68	1	8
β-strand	71-73	3	10
α-helix	78-80	3
β-strand	82-90	9	9
α-helix	94-96	3
β-strand	98-100	3	9
β-strand	104-109	6	9
β-strand	118-124	7	12
β-strand	131-136	6	12
α-helix	143-145	3
β-strand	153-154	2	12
α-helix	155-157	3
β-strand	158-162	5	12
α-helix	163-165	3
β-strand	167-175	9	12
β-strand	196-197	2	12

Chain E: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-5	3	13
β-strand	8-12	5	14
β-strand	17-22	6	13
α-helix	23	1
β-strand	29-35	7	14
β-strand	42-48	7	14
β-strand	51-54	4	14
β-strand	63-66	4	13
β-strand	73-77	5	13
α-helix	82-84	3
β-strand	86-93	8	14
β-strand	104-105	2	14
β-strand	109-114	6	14
α-helix	117-119	3
β-strand	121	1	15
α-helix	122-123	2
β-strand	124-129	6	12
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-150	11	12
β-strand	151	1	15
β-strand	155-161	7	16
β-strand	164-166	3	16
β-strand	170-172	3	12
α-helix	176	1
β-strand	177-178	2	12
β-strand	188-197	10	12
α-helix	198-201	4
β-strand	207-214	8	16
β-strand	217	1	17
α-helix	228-229	2
β-strand	231	1	17
β-strand	233-240	8	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen, A-2 alpha chain	A	protein	275	Homo sapiens	A0A140T913 (AlphaFold model)
Beta-2-microglobulin	B	protein	100	Homo sapiens	P61769 (AlphaFold model)
Spike protein S2	C	protein	9	Severe acute respiratory syndrome coronavirus 2	P0DTC2 (AlphaFold model)
pRLQ3 T cell receptor alpha chain	D	protein	204	Homo sapiens
pRLQ3 T cell receptor beta chain	E	protein	244	Homo sapiens

Sequence of entity 1 (A), FASTA

>7N1E_1 MHC class I antigen, A-2 alpha chain (chains A)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B), FASTA

>7N1E_2 Beta-2-microglobulin (chains B)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C), FASTA

>7N1E_3 Spike protein S2 (chains C)
RLQSLQTYV

Sequence of entity 4 (D), FASTA

>7N1E_4 pRLQ3 T cell receptor alpha chain (chains D)
QRVTQPEKLLSVFKGAPVELKCNYSYSGSPELFWYVQYSRQRLQLLLRHISRESIKGFTA
DLNKGETSFHLKKPFAQEEDSAMYYCALSGFNNAGNMLTFGGGTRLMVKPNIQNPDPAVY
QLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSNKSD
FACANAFNNSIIPEDTFFPSPESS

Sequence of entity 5 (E), FASTA

>7N1E_5 pRLQ3 T cell receptor beta chain (chains E)
GVAQSPRYKIIEKRQSVAFWCNPISGHATLYWYQQILGQGPKLLIQFQNNGVVDDSQLPK
DRFSAERLKGVDSTLKIQPAKLEDSAVYLCASSLGGAGGADTQYFGPGTRLTVLEDLKNV
FPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPLKEQ
PALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRAD

Primary citation

Structural assessment of HLA-A2-restricted SARS-CoV-2 spike epitopes recognized by public and private T-cell receptors. Wu, D., Kolesnikov, A., Yin, R. et al. Nat Commun (2022) 13:19-19. DOI 10.1038/s41467-021-27669-8 · PubMed

Other PDB entries of the same protein (UniProt A0A140T913 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6O53 1.4 Å, Structure of HLA-A2:01 with peptide MM96
6O4Z 1.5 Å, Structure of HLA-A2:01 with peptide MM92
7QPJ 1.54 Å, Crystal structure of engineered TCR (756) complexed to HLA-A*02:01 presenting MAGE-A10…
6O51 1.55 Å, Structure of HLA-A2:01 with peptide MM90
6O4Y 1.58 Å, Structure of HLA-A2:01 with peptide MM91
7MJ7 1.6 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7P3D 1.67 Å, MHC I A02 Allele presenting YLQPRTFLL
7MJ9 1.75 Å, HLA-A*02:01 bound to Neuroblastoma Derived mutant IGFBPL1 peptide
7MJ8 1.79 Å, HLA-A*02:01 bound to Neuroblastoma Derived IGFBPL1 peptide
7SA2 1.85 Å, SARS-CoV-2 spike-derived peptide S1060-1068 (VVFLHVTYV) presented by HLA-A*02:01
2P5E 1.89 Å, Crystal Structures of High Affinity Human T-Cell Receptors Bound to pMHC Reveal Native…
7MKB 1.9 Å, Human leukocyte antigen A*0201 in complex with SARS-CoV-2 epitope YLQPRTFLL

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