9HKQ | pdb_00009hkq

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

• PDB DOI: https://doi.org/10.2210/pdb9HKQ/pdb
• EM Map EMD-52234: EMDB EMDataResource

• Classification: PROTEIN BINDING
• Organism(s): Mus musculus, Homo sapiens, synthetic construct
• Expression System: Homo sapiens, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-12-04 Released: 2025-12-17 
• Deposition Author(s): Jie, B., Shenghai, C., Liqiang, P., Xing, Z.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Targeting Intracellular Antigen with TCR-Mimic Single-Domain Antibody for Cancer Immunotherapy

Jie, B., Shanghai, C., Xinyu, G., Yanping, S., Linling, Z., Lingxiao, J., Shuqing, C., Xinlei, Z., Xing, Z., Liqiang, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 103.51 kDa 
• Atom Count: 7,256 
• Modeled Residue Count: 924 
• Deposited Residue Count: 928 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BM17 antibody heavy chain	A [auth D]	224	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BM17 antibody light chain	B [auth E]	209	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	C	99	Homo sapiens	Mutation(s): 0  Gene Names: B2M, CDABP0092, HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens) Explore P61769  Go to UniProtKB:  P61769
PHAROS:  P61769 GTEx:  ENSG00000166710

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	D [auth B]	274	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for Q8WLS4 (Homo sapiens) Explore Q8WLS4  Go to UniProtKB:  Q8WLS4

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Cancer/testis antigen 1	E [auth A]	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P78358 (Homo sapiens) Explore P78358  Go to UniProtKB:  P78358
PHAROS:  P78358 GTEx:  ENSG00000184033 ENSG00000268651

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
single domain antibody VHH5	F	113	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Jie, B., Shenghai, C., Liqiang, P., Xing, Z.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release