9HKQ: VHH5 targeting NY-ESO-1(SLLMWITQC)/HLA-A*02:01

Structure of VHH5 targeting NY-ESO-1(SLLMWITQC)/HLA-A*02:01. Determined by electron microscopy at 3.3 Å resolution. Released 17 Dec 2025.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Mus musculus, Homo sapiens, synthetic construct
Chains: 6
Atoms: 7,256
Mol. weight: 103.51 kDa
Released: 17 Dec 2025

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

Secondary structure: helices and β-sheets

9HKQ contains 25 α-helices and 85 β-strands across 5 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 B: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-12	10	14
α-helix	20	1
β-strand	21-28	8	14
β-strand	31-37	7	14
α-helix	45	1
β-strand	46-47	2	14
α-helix	50-52	3
α-helix	57-84	28
β-strand	94-103	10	14
β-strand	109-118	10	14
β-strand	121-126	6	14
β-strand	133-135	3	14
α-helix	141-149	9
α-helix	152-158	7
α-helix	159-164	6
α-helix	165-174	10
β-strand	183	1	15
α-helix	184-185	2
β-strand	186-193	8	16
β-strand	199-208	10	16
β-strand	209	1	15
β-strand	214-219	6	17
β-strand	223	1	17
β-strand	229-230	2	16
β-strand	234-235	2	16
β-strand	241-249	9	16
α-helix	254-256	3
β-strand	257-262	6	17
β-strand	270-272	3	17

Chain C: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	11
β-strand	6-11	6	12
β-strand	21-30	10	12
β-strand	31	1	11
β-strand	35-41	7	13
β-strand	44-45	2	13
α-helix	46	1
β-strand	51	1	12
β-strand	55-56	2	12
β-strand	62-70	9	12
β-strand	78-84	7	13
β-strand	91-94	4	13
α-helix	95-96	2

Chain D: 6 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	17-25	9	1
β-strand	34-41	8	3
β-strand	48-54	7	3
β-strand	59-61	3	3
α-helix	63-65	3
β-strand	69-74	6	1
β-strand	79-85	7	1
α-helix	89-91	3
β-strand	93-101	9	3
β-strand	108-112	5	3
β-strand	116-118	3	3
β-strand	119-120	2	2
β-strand	126	1	4
β-strand	129-132	4	5
α-helix	134-136	3
β-strand	144-146	3	6
β-strand	149-154	6	5
β-strand	155	1	4
β-strand	161-163	3	7
β-strand	172-174	3	5
α-helix	175-177	3
β-strand	178-179	2	5
β-strand	185-191	7	5
β-strand	192-194	3	6
α-helix	195-197	3
β-strand	203-209	7	7
α-helix	210-212	3
β-strand	214-220	7	7

Chain E: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	8
β-strand	10-13	4	3
β-strand	19-29	11	8
β-strand	33-37	5	3
β-strand	44-49	6	3
β-strand	52-53	2	3
β-strand	61-74	14	8
α-helix	79-81	3
β-strand	84-89	6	3
β-strand	96-97	2	3
β-strand	101-105	5	3
β-strand	113-117	5	9
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	9
β-strand	144-148	5	10
β-strand	153-154	2	10
β-strand	158-162	5	9
α-helix	163-166	4
β-strand	172-181	10	9
α-helix	182-186	5
β-strand	191-196	6	10
β-strand	204-208	5	10

Chain F: 2 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	18
β-strand	7	1	19
β-strand	10-12	3	20
β-strand	17-22	6	19
β-strand	24-25	2	18
α-helix	30-32	3
β-strand	33-39	7	20
β-strand	46-52	7	20
β-strand	57-59	3	20
β-strand	67-71	5	19
β-strand	78-83	6	19
α-helix	87-89	3
β-strand	91-97	7	20
β-strand	102-103	2	20
β-strand	108-111	4	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
BM17 antibody heavy chain	D	protein	224	Mus musculus
BM17 antibody light chain	E	protein	209	Mus musculus
Beta-2-microglobulin	C	protein	99	Homo sapiens	P61769 (AlphaFold model)
MHC class I antigen	B	protein	274	Homo sapiens	Q8WLS4 (AlphaFold model)
Cancer/testis antigen 1	A	protein	9	Homo sapiens	P78358 (AlphaFold model)
single domain antibody VHH5	F	protein	113	synthetic construct

Sequence of entity 1 (D), FASTA

>9HKQ_1 BM17 antibody heavy chain (chains D)
QVTLKESGPGILQPSQTLSLTCSFSGFSLSTSGMGVSWIRQPSGKGLEWLAHIYWDDDKR
YNPSLKSRLTISKDTSSNQVFLKITSVDTADTATYYCARVYYGYDGGFFDYWGQGTTLTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKS

Sequence of entity 2 (E), FASTA

>9HKQ_2 BM17 antibody light chain (chains E)
QIVLTQSPAIMSASPGEKVTITCSASSSVSYMHWFQQKPGTSPKLWIYSTSNLASGVPAR
FSGSGSGTSYSLTISRMEAEDAATYYCHQRSSYPLTFGAGTKLEIKRTVAAPSVFIFPPS
DEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTL
SKADYEKHKVYACEVTHQGLSSPVTKSFN

Sequence of entity 3 (C), FASTA

>9HKQ_3 Beta-2-microglobulin (chains C)
IQRTPKIQVYSRHPAENGKSNFLNCYVSGFHPSDIEVDLLKNGERIEKVEHSDLSFSKDW
SFYLLYYTEFTPTEKDEYACRVNHVTLSQPKIVKWDRDM

Sequence of entity 4 (B), FASTA

>9HKQ_4 MHC class I antigen (chains B)
GSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYW
DGETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDG
KDYIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQ
RTDAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGT
FQKWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRW

Sequence of entity 5 (A), FASTA

>9HKQ_5 Cancer/testis antigen 1 (chains A)
SLLMWITQC

Sequence of entity 6 (F), FASTA

>9HKQ_6 single domain antibody VHH5 (chains F)
QVQLQESGGGLVQAGGSLRLSCAASGNISAVYTMGWYRQAPGKEREFVAAIDYGGSTYYA
DSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCASYYHGYWGQGTQVTVSS

Primary citation

Targeting Intracellular Antigen with TCR-Mimic Single-Domain Antibody for Cancer Immunotherapy. Jie, B., Shanghai, C., Xinyu, G. et al. To be published.

Other PDB entries of the same protein (UniProt P61769 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4E0K 0.97 Å, Crystal Structure of the amyloid-fibril forming peptide KDWSFY derived from human Beta 2…
1K5N 1.09 Å, HLA-B*2709 bound to nona-peptide M9
3MRE 1.1 Å, Crystal Structure of MHC class I HLA-A2 molecule complexed with EBV bmlf1-280-288…
2YXF 1.13 Å, The high resolution crystal structure of beta2-microglobulin under physiological…
8E2Z 1.13 Å, Structures of HLA-B8E76C loaded with long peptides reveal novel features at the…
7NMR 1.15 Å, Crystal structure of beta-2-microglobulin D76S mutant
8ROP 1.15 Å, Crystal structure of HLA B*18:01 in complex with QEIRTFSF, an 8-mer epitope from…
7R7W 1.17 Å, Crystal structure of HLA-B*5301 complex with an HIV-1 Gag-derived epitope QW9 S3T variant
4U1M 1.18 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…
3CZF 1.2 Å, Crystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide…
6Y26 1.2 Å, Crystal structure of HLA-B2705 complexed with the nona-peptide mA
7NMC 1.2 Å, Crystal structure of beta-2-microglobulin D76E mutant

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