9XME: MHC class I antigen

Complex of HLA-A2, a class I MHC, with a wild type UTP20 peptide. Determined by X-ray diffraction at 2.04 Å resolution. Released 23 Sept 2026.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,031
Mol. weight: 89.65 kDa
Released: 23 Sept 2026

Explore 9XME in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XME contains 28 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: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	1
α-helix	21	1
β-strand	22-29	8	1
β-strand	32-38	7	1
β-strand	47-48	2	1
α-helix	51-53	3
α-helix	58-85	28
β-strand	95-104	10	1
β-strand	110-119	10	1
β-strand	122-127	6	1
β-strand	134-136	3	1
α-helix	139-150	12
α-helix	153-159	7
α-helix	160-164	5
α-helix	165-175	11
α-helix	177-180	4
β-strand	184	1	2
α-helix	185-186	2
β-strand	187-196	10	3
β-strand	199-209	11	3
β-strand	210	1	2
β-strand	215-220	6	4
β-strand	223-224	2	4
α-helix	226-228	3
β-strand	230-231	2	3
α-helix	232-234	3
β-strand	235-236	2	3
β-strand	242-251	10	3
α-helix	255-257	3
β-strand	258-263	6	4
β-strand	271-274	4	4

Chain B: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	5-6	2
β-strand	7-12	6	6
β-strand	22-31	10	6
β-strand	32	1	5
β-strand	37-42	6	7
β-strand	45-46	2	7
β-strand	51-52	2	6
α-helix	53-55	3
β-strand	56-57	2	6
β-strand	63-71	9	6
β-strand	79-84	6	7
β-strand	92-95	4	7

Chain D: 12 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-13	10	8
α-helix	21	1
β-strand	22-29	8	8
β-strand	32-38	7	8
β-strand	47-48	2	8
α-helix	51-53	3
α-helix	58-85	28
β-strand	95-104	10	8
β-strand	110-119	10	8
β-strand	122-127	6	8
β-strand	134-136	3	8
α-helix	139-150	12
α-helix	153-159	7
α-helix	160-164	5
α-helix	165-175	11
α-helix	177-180	4
β-strand	184	1	9
α-helix	185-186	2
β-strand	187-194	8	10
β-strand	199-209	11	10
β-strand	210	1	9
β-strand	215-220	6	11
β-strand	223-224	2	11
α-helix	226-228	3
β-strand	230-231	2	10
α-helix	232-234	3
β-strand	235-236	2	10
β-strand	242-251	10	10
α-helix	255-257	3
β-strand	258-263	6	11
β-strand	271-273	3	11

Chain E: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	12
α-helix	5-6	2
β-strand	7-12	6	13
β-strand	22-31	10	13
β-strand	32	1	12
β-strand	37-42	6	14
β-strand	45-46	2	14
α-helix	47	1
β-strand	51-52	2	13
β-strand	56-57	2	13
β-strand	63-71	9	13
β-strand	79-84	6	14
β-strand	92-95	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, D	protein	276	Homo sapiens	Q8WLS4 (AlphaFold model)
Beta-2-microglobulin	B, E	protein	100	Homo sapiens	P61769 (AlphaFold model)
Small subunit processome component 20 homolog	C, F	protein	9	Homo sapiens	O75691

Sequence of entity 1 (A, D), FASTA

>9XME_1 MHC class I antigen (chains A, D)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, E), FASTA

>9XME_2 Beta-2-microglobulin (chains B, E)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, F), FASTA

>9XME_3 Small subunit processome component 20 homolog (chains C, F)
AMDLGIDKV

Primary citation

Structural basis for CD8 + T cell recognition of the charge-reversed neoantigen UTP20 D2661H . Wang, J., Li, S., Mao, L. et al. J Struct Biol (2026) 218:108371-108371. DOI 10.1016/j.jsb.2026.108371 · PubMed

Other PDB entries of the same protein (UniProt Q8WLS4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9X7U 1.59 Å, Complex of HLA-A2, a class I MHC, with a UTP20 peptide
9WK0 1.8 Å, Neoantigen Rac1P29S-HLA-A2
21GJ 1.83 Å, Neoantigen p53Y220D-HLA-A2
21EX 2.02 Å, Wild tipe p53WT-HLA-A2
9J4U 2.17 Å, Structural basis for recognition of SARS-CoV-2 conserved nucleocapside epitopes by…
9PIX 2.35 Å, Mur14 Fab with HBV c18V pMHC
9PKC 2.5 Å, Mur35 Fab with HBV c18V pMHC
9PKF 2.6 Å, Mur35 Fab with HBV c18I pMHC
9PKV 2.72 Å, HU-38 Fab with PRAME pMHC
9LLU 2.87 Å, p53 epitope specific TCR 4414A binding to p53Y220D-HLA-A2
3HG1 3.0 Å, Germline-governed recognition of a cancer epitope by an immunodominant human T cell…
9C96 3.0 Å, Cryo-EM structure of TAP binding protein related (TAPBPR) in complex with HLA-A*02:01…

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