8ESB: HLA-A2

CryoEM structure of HLA-A2 bound to MAGEA8 (232-241) peptide. Determined by electron microscopy at 3.12 Å resolution. Released 3 May 2023.

Method: Electron microscopy
Resolution: 3.12 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,140
Mol. weight: 150.92 kDa
Released: 3 May 2023

Explore 8ESB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ESB contains 8 α-helices and 32 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: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	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	57-83	27
β-strand	94-103	10	1
β-strand	109-118	10	1
β-strand	121-125	5	1
β-strand	126	1	2
β-strand	133	1	2
α-helix	138-148	11
α-helix	152-161	10
α-helix	163-174	12
α-helix	176-179	4
β-strand	183	1	3
α-helix	184-185	2
β-strand	186-191	6	4
β-strand	198-208	11	4
β-strand	209	1	3
β-strand	213-219	7	5
β-strand	222-223	2	5
β-strand	229-230	2	4
β-strand	234-235	2	4
β-strand	241-250	10	4
β-strand	257-263	7	5
β-strand	270-272	3	5

Chain B: 1 helix, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	6
β-strand	6-11	6	7
α-helix	14-15	2
β-strand	21-30	10	7
β-strand	31	1	6
β-strand	36-41	6	8
β-strand	44-45	2	8
β-strand	50-51	2	7
β-strand	55-56	2	7
β-strand	62-63	2	7
β-strand	66-70	5	7
β-strand	78-83	6	8
β-strand	91-94	4	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Beta-2-microglobulin,HLA class I antigen,MAGE-A8 peptide chimera	A, B, C	protein	448	Homo sapiens	Q53Z42 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>8ESB_1 Beta-2-microglobulin,HLA class I antigen,MAGE-A8 peptide chimera (chains A, B, C)
GLYDGREHSVGCGGSGGGGSGGGGSIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDI
EVDLLKNGERIEKVEHSDLSFSKDWSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKW
DRDMGGGGSGGGGSGGGGSGGGGSGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASQRMEPRAPWIEQEGPEYWDGETRKVKAHSQTHRVDLGTLRGCYNQSEAGSHTVQ
RMYGCDVGSDWRFLRGYHQYAYDGKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQL
RAYLEGTCVEWLRRYLENGKETLQRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLT
WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEP
EQKLISEEDLGGEQKLISEEDLHHHHHH

Primary citation

Structural analysis of cancer-relevant TCR-CD3 and peptide-MHC complexes by cryoEM. Saotome, K., Dudgeon, D., Colotti, K. et al. Nat Commun (2023) 14:2401-2401. DOI 10.1038/s41467-023-37532-7 · PubMed

Other PDB entries of the same protein (UniProt Q53Z42 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6TRN 1.35 Å, Crystal structure of HLA A2*01-AVYDGREHTV
8FU4 1.6 Å, HCMV US11 peptide binding to HLA-A*02:01
7UM2 1.63 Å, SARS-CoV-2 Spike-derived peptide S417-425 K417T mutant (TIADYNYKL) presented by…
7U1R 1.8 Å, SARS-CoV-2 Spike-derived peptide S1185-1193 K1191N mutant (RLNEVANNL) presented by…
8RBV 1.8 Å, SARS-CoV-2 Spike-derived peptide S976-984 S982A mutant (VLNDILARL) presented by…
22EE 1.99 Å, Structure of HLA-A2:01 with 9-mer peptide PGS
7RTD 2.05 Å, SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL) presented by HLA-A*02:01
9MIN 2.05 Å, Structure of a designed minibinder to NYESO1-A*02:01
7UR1 2.17 Å, SARS-CoV-2 Spike-derived peptide S1215-1224 (YIWLGFIAGL) presented by HLA-A*02:01
7RTR 2.6 Å, YLQ-SG3 TCR in complex with SARS-CoV-2 Spike-derived peptide S269-277 (YLQPRTFLL)…
8TBV 2.64 Å, Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL
6TRO 3.0 Å, Crystal structure of the T-cell receptor GVY01 bound to HLA A2*01-GVYDGREHTV

Browse structure collections

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