9K2I: MHC class I antigen

Rac1 epitope specific TCR 5934 binding to Rac1P29S-HLA-A2. Determined by X-ray diffraction at 3.05 Å resolution. Released 22 Oct 2025.

Method: X-ray diffraction
Resolution: 3.05 Å
Organism: Homo sapiens
Chains: 20
Atoms: 26,756
Mol. weight: 383.5 kDa
Released: 22 Oct 2025

Explore 9K2I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9K2I contains 75 α-helices and 317 β-strands across 19 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: 8 helices, 18 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	50-53	4
α-helix	57-85	29
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	153-157	5
α-helix	158-163	6
α-helix	164-174	11
α-helix	176-179	4
β-strand	183	1	2
β-strand	188-192	5	3
β-strand	198-208	11	3
β-strand	209	1	2
β-strand	213-217	5	4
β-strand	229-230	2	3
β-strand	234-235	2	3
β-strand	241-250	10	3
α-helix	254-256	3
β-strand	259-263	5	4
β-strand	270-272	3	4

Chains B, L and Q: 1 helix, 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
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: 4 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-8	5	44
β-strand	11-15	5	45
β-strand	20-27	8	44
β-strand	33	1	46
β-strand	34-39	6	45
β-strand	46-51	6	45
β-strand	57-60	4	44
β-strand	63-68	6	44
α-helix	69-71	3
β-strand	73-78	6	44
β-strand	87-91	5	45
β-strand	92-93	2	47
β-strand	94	1	46
α-helix	99-101	3
β-strand	102-103	2	47
β-strand	107-112	6	45
α-helix	113-114	2
β-strand	121-125	5	48
β-strand	126	1	49
β-strand	135-139	5	48
β-strand	155-157	3	48
β-strand	161-165	5	48
α-helix	166-168	3
β-strand	170-179	10	48
β-strand	200	1	48

Chain E: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	50
β-strand	12-14	3	51
β-strand	18-21	4	52
β-strand	22-25	4	50
β-strand	31-37	7	53
β-strand	43-50	8	53
β-strand	53-54	2	53
β-strand	65-67	3	52
β-strand	73	1	50
β-strand	75-79	5	52
α-helix	83-85	3
β-strand	87-93	7	53
α-helix	104-105	2
β-strand	106-107	2	53
β-strand	111-113	3	53
β-strand	114-116	3	51
α-helix	119-121	3
β-strand	123	1	54
α-helix	124-125	2
β-strand	126-130	5	55
β-strand	131	1	49
α-helix	132-133	2
α-helix	134-140	7
β-strand	142-152	11	55
β-strand	153	1	54
β-strand	157-163	7	56
β-strand	166-168	3	56
β-strand	172-174	3	55
β-strand	179-180	2	55
β-strand	190-199	10	55
α-helix	200-203	4
β-strand	209-216	8	56
β-strand	219	1	57
β-strand	233	1	57
β-strand	235-242	8	56

Chain F: 9 helices, 16 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	50-53	4
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	138-150	13
α-helix	152-157	6
α-helix	158-164	7
α-helix	165-174	10
α-helix	176-179	4
α-helix	183-185	3
β-strand	186-192	7	9
β-strand	198-208	11	9
β-strand	214-218	5	10
β-strand	229-230	2	9
β-strand	234-235	2	9
β-strand	241-250	10	9
β-strand	258-262	5	10
β-strand	270-272	3	10

Chain G: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	11
α-helix	4-5	2
β-strand	6-11	6	12
β-strand	21-30	10	12
β-strand	31	1	11
β-strand	36-41	6	13
β-strand	44-45	2	13
β-strand	50-51	2	12
α-helix	52-54	3
β-strand	55-56	2	12
β-strand	62-70	9	12
β-strand	78-83	6	13
β-strand	91-94	4	13

Chains H, M and R: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	8	1	14

Chain I: 2 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5-8	4	39
β-strand	11-15	5	40
β-strand	20-26	7	39
β-strand	33	1	41
β-strand	34-39	6	40
β-strand	46-51	6	40
β-strand	57-60	4	39
β-strand	63-68	6	39
β-strand	73-78	6	39
β-strand	87-91	5	40
β-strand	92-93	2	18
β-strand	94	1	41
α-helix	100-101	2
β-strand	102-103	2	18
β-strand	107-112	6	40
α-helix	113-114	2
β-strand	121-125	5	42
β-strand	126	1	21
β-strand	134-139	6	42
β-strand	156-157	2	42
β-strand	162-164	3	43
β-strand	171-173	3	43
β-strand	174-179	6	42
β-strand	200	1	42

7 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MHC class I antigen	A, F, K, P	protein	276	Homo sapiens	Q8WLS4 (AlphaFold model)
Beta-2-microglobulin	B, G, L, Q	protein	100	Homo sapiens	P61769 (AlphaFold model)
Phe-ser-gly-glu-tyr-ile-pro-thr-val	C, H, M, R	protein	9	Homo sapiens
T cell receptor 5934 chain beta	E, J, O, T	protein	247	Homo sapiens
T cell receptor5934 chain alpha	D, I, N, S	protein	207	Homo sapiens

Sequence of entity 1 (A, F, K, P), FASTA

>9K2I_1 MHC class I antigen (chains A, F, K, P)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWE

Sequence of entity 2 (B, G, L, Q), FASTA

>9K2I_2 Beta-2-microglobulin (chains B, G, L, Q)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (C, H, M, R), FASTA

>9K2I_3 PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL (chains C, H, M, R)
FSGEYIPTV

Sequence of entity 4 (E, J, O, T), FASTA

>9K2I_4 T cell receptor 5934 chain beta (chains E, J, O, T)
MDTAVSQTPKYLVTQMGNDKSIKCEQNLGHDTMYWYKQDSKKFLKIMFSYNNKELIINET
VPNRFSPKSPDKAHLNLHINSLELGDSAVYFCASSQLAGGPLYNEQFFGPGTRLTVLEDL
KNVFPPEVAVFEPSEAEISHTQKATLVCLATGFYPDHVELSWWVNGKEVHSGVCTDPQPL
KEQPALNDSRYALSSRLRVSATFWQNPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSA
EAWGRAD

Sequence of entity 5 (D, I, N, S), FASTA

>9K2I_5 T cell receptor5934 chain alpha (chains D, I, N, S)
MGENVEQHPSTLSVQEGDSAVIKCTYSDSASNYFPWYKQELGKGPQLIIDIRSNVGEKKD
QRIAVTLNKTAKHFSLHITETQPEDSAVYFCAASRGGAQKLVFGQGTRLTINPNIQNPDP
AVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSN
KSDFACANAFNNSIIPEDTFFPSPESS

Primary citation

Structural basis for TCR recognition of a Rac1 neoantigen arising from anchor residue mutation. Zeng, Y., Yang, D., Zhao, J. et al. J Struct Biol (2026) 218:108329-108329. DOI 10.1016/j.jsb.2026.108329 · 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
9XME 2.04 Å, Complex of HLA-A2, a class I MHC, with a wild type UTP20 peptide
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…

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