9Z51: HPV_Jin TCR

HPV_Jin TCR in complex with HLA-A*02:01 presenting HPV16 E7 9mer peptide (11-YMLDLQPET-19). Determined by X-ray diffraction at 3.13 Å resolution. Released 16 Sept 2026.

Method: X-ray diffraction
Resolution: 3.13 Å
Organisms: Homo sapiens, Human papillomavirus 16
Chains: 20
Atoms: 25,248
Mol. weight: 393.17 kDa
Ligands: NAG
Released: 16 Sept 2026

Explore 9Z51 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Z51 contains 89 α-helices and 295 β-strands across 16 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: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	9
β-strand	17-22	6	10
β-strand	30-36	7	9
α-helix	41-42	2
β-strand	43-48	6	9
β-strand	52-56	5	10
β-strand	59-64	6	10
β-strand	69-74	6	10
α-helix	79-81	3
β-strand	84-90	7	9
β-strand	96-98	3	9
β-strand	102-107	6	9
β-strand	116-122	7	11
β-strand	129-134	6	11
α-helix	143-145	3
β-strand	151-152	2	11
α-helix	153-155	3
β-strand	158-160	3	12
α-helix	161-163	3
β-strand	165-167	3	12
β-strand	169-173	5	11
β-strand	195	1	11
α-helix	197-199	3

Chain B: 8 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	13
β-strand	8-12	5	14
β-strand	19-22	4	13
α-helix	23-24	2
β-strand	29-35	7	14
β-strand	42-47	6	14
β-strand	52-55	4	14
β-strand	62-66	5	13
β-strand	72-76	5	13
α-helix	81-83	3
β-strand	85-92	8	14
α-helix	94-96	3
α-helix	98-101	4
β-strand	104-105	2	14
β-strand	109-114	6	14
β-strand	121	1	15
α-helix	122-123	2
β-strand	124-129	6	11
α-helix	130-131	2
α-helix	132-138	7
β-strand	140-142	3	16
β-strand	144-150	7	11
β-strand	151	1	15
β-strand	155-161	7	17
β-strand	165	1	17
β-strand	170-172	3	11
β-strand	177-178	2	11
β-strand	188-194	7	11
β-strand	195-197	3	16
α-helix	198-202	5
β-strand	207-214	8	17
β-strand	217	1	18
β-strand	231	1	18
β-strand	233-240	8	17

Chain C: 9 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	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	140-150	11
α-helix	153-159	7
α-helix	160-164	5
α-helix	165-175	11
β-strand	184	1	2
α-helix	185-186	2
β-strand	187-193	7	3
β-strand	199-209	11	3
β-strand	210	1	2
β-strand	215-220	6	4
β-strand	223-225	3	4
β-strand	229-231	3	3
α-helix	232-234	3
β-strand	235-236	2	3
β-strand	242-251	10	3
α-helix	254-256	3
β-strand	258-263	6	4
β-strand	271-273	3	4

Chain D: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	5
β-strand	26	1	6
β-strand	29-31	3	7
β-strand	41-45	5	7
β-strand	48-50	3	6
β-strand	51	1	5
β-strand	55-61	7	8
β-strand	65	1	8
β-strand	70-71	2	7
α-helix	72-74	3
β-strand	75-76	2	6
β-strand	82-83	2	6
β-strand	86-90	5	7
β-strand	98-104	7	8
β-strand	111-114	4	8

Chain E: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	8-12	5	26
β-strand	17-22	6	27
β-strand	31-36	6	26
α-helix	41-42	2
β-strand	43-48	6	26
β-strand	52-56	5	27
β-strand	59-64	6	27
β-strand	69-74	6	27
α-helix	79-81	3
β-strand	83-90	8	26
β-strand	96-98	3	26
β-strand	102-107	6	26
β-strand	116-121	6	28
β-strand	122	1	29
β-strand	129-134	6	28
α-helix	143-145	3
β-strand	150-152	3	28
β-strand	158-159	2	30
β-strand	166-167	2	30
β-strand	169-174	6	28
α-helix	181-184	4
β-strand	195	1	28

Chain F: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	31
β-strand	8-12	5	32
β-strand	17-21	5	33
β-strand	22	1	31
α-helix	23-24	2
β-strand	29-35	7	32
β-strand	42-47	6	32
β-strand	52-55	4	32
β-strand	62-66	5	33
β-strand	72-76	5	33
α-helix	81-83	3
β-strand	85-92	8	32
α-helix	98-101	4
β-strand	104-105	2	32
β-strand	109-114	6	32
β-strand	121	1	34
α-helix	122-123	2
β-strand	124-128	5	29
α-helix	129-131	3
α-helix	132-138	7
β-strand	140-150	11	29
β-strand	151	1	34
β-strand	155-161	7	35
β-strand	165-166	2	35
β-strand	170-172	3	29
β-strand	177-178	2	29
β-strand	188-197	10	29
α-helix	198-202	5
β-strand	207-214	8	35
β-strand	217	1	36
β-strand	231	1	36
β-strand	233-240	8	35

Chain G: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-15	12	19
β-strand	19-29	11	19
β-strand	32-38	7	19
β-strand	47-48	2	19
α-helix	58-86	29
β-strand	95-104	10	19
β-strand	110-119	10	19
β-strand	123-127	5	19
β-strand	134-136	3	19
α-helix	141-150	10
α-helix	153-159	7
α-helix	160-164	5
α-helix	165-175	11
β-strand	184	1	20
α-helix	185-186	2
β-strand	190-194	5	21
β-strand	200-209	10	21
β-strand	210	1	20
β-strand	214-220	7	22
β-strand	223-224	2	22
β-strand	229-231	3	21
α-helix	232-234	3
β-strand	235-236	2	21
β-strand	242-250	9	21
α-helix	255-257	3
β-strand	258-264	7	22
β-strand	271-273	3	22

Chain H: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	21-23	3	23
β-strand	26	1	24
β-strand	29-31	3	24
β-strand	43-50	8	24
β-strand	51	1	23
β-strand	56-61	6	25
β-strand	64-65	2	25
α-helix	66	1
β-strand	70-71	2	24
α-helix	72-74	3
β-strand	75-76	2	24
β-strand	82-88	7	24
β-strand	99-103	5	25
β-strand	111-114	4	25

8 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	C, G, L, S	protein	303	Homo sapiens	Q8WLS4 (AlphaFold model)
Beta-2-microglobulin	D, H, M, T	protein	100	Homo sapiens	P61769 (AlphaFold model)
HPV_Jin TCR alpha chain (TRAV1-2*03)	A, E, J, Q	protein	200	Homo sapiens
HPV_Jin TCR beta chain (TRBV5-6*01)	B, F, K, R	protein	243	Homo sapiens
Protein E7	I, N, P, U	protein	9	Human papillomavirus 16	P03129 (AlphaFold model)

Sequence of entity 1 (C, G, L, S), FASTA

>9Z51_1 MHC class I antigen (chains C, G, L, S)
MGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEY
WDGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYD
GKDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETL
QRTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDG
TFQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPGSGGSGGSAGGGLNDIFEAQKIE
WHE

Sequence of entity 2 (D, H, M, T), FASTA

>9Z51_2 Beta-2-microglobulin (chains D, H, M, T)
MIQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKD
WSFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 3 (A, E, J, Q), FASTA

>9Z51_3 HPV_Jin TCR alpha chain (TRAV1-2*03) (chains A, E, J, Q)
QNIDQPTEMTATEGAIVQINCTYQTSGFNGLFWYQQHAGEAPTFLSYNVLDGLEEKGRFS
SFLSRSKGYSYLLLKELQMKDSASYLCASVDGNNRLAFGKGNQVVVIPYIQNPDPAVYQL
RDSKSSDKFVCLFTDFDSQIQVSQSKDSDVYITDKCVLDMRSMDFKSNSAVAWSQKSDFT
CANAFQNSIIPEDTFFPSPE

Sequence of entity 4 (B, F, K, R), FASTA

>9Z51_4 HPV_Jin TCR beta chain (TRBV5-6*01) (chains B, F, K, R)
GVTQSPTHLIKTRGQQVTLRCSPKSGHDTVSWYQQALGQGPQFIFQYYEEEERQRGNFPD
RFSGHQFPNYSSELNVNALLLGDSALYLCASSLGWRGGRYNEQFFGPGTRLTVLEDLKNV
FPPEVAVFEPSKAEISRTQKATLVCLATGFYPPHVELSWWVNGKEVHDGVCTDPQPLKEQ
PALQDSRYALSSRLRVSATFWQDPRNHFRCQVQFYGLSENDEWTQDRAKPVTQIVSAEAW
GRA

Sequence of entity 5 (I, N, P, U), FASTA

>9Z51_5 Protein E7 (chains I, N, P, U)
YMLDLQPET

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	9

Water and common crystallization additives (SO4) are not listed.

Primary citation

HPV16 E7-specific NCI TCR in complex with HLA-A*02:01 presenting HPV16 E7 9mer peptide (11-YMLDLQPET-19). Jackson, E. To be published.

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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