9WFS | pdb_00009wfs

Crystal structure of 3-2E TCR in complex with HLA-A*11:01 bound to A0PXA8 peptide(ITGAVGIAK)

PDB DOI: https://doi.org/10.2210/pdb9WFS/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Homo sapiens, Clostridium novyi NT
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2025-08-22 Released: 2026-08-26
Deposition Author(s): Jin, X.Y., Zhang, Z.Y., Xi, Y.H., Gu, Y.H., Qi, J.X., Chai, Y., Tan, S.G., Gao, G.F.
Funding Organization(s): Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.297 (Depositor), 0.296 (DCC)
R-Value Work:
0.240 (Depositor), 0.238 (DCC)
R-Value Observed:
0.242 (Depositor)

Starting Models: experimental, in silico
View more details

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Commensal Clostridium spp. harbor mimetic CTL-epitopes eliciting T cells cross-recognizing KRAS-G12V tumor neoantigen

Jin, X.Y., Wang, W.L., Zhang, Z.Y., Gu, Y.H., Xi, Y.H., Jiang, M., Peng, Y.Q., Yao, P.J., Tang, L.F., Ma, K.K., Wang, J., Li, F.Y., Li, X.W., Jin, W.J., Chen, Y., Chai, Y., Qi, J.X., Zhang, C.W.H., Liu, K.F., Wang, J., Gao, G.F., Tan, S.G.

To be published.

Macromolecule Content

Total Structure Weight: 97.52 kDa
Atom Count: 6,621
Modeled Residue Count: 822
Deposited Residue Count: 866
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-2E TCR alpha chain	A	220	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
3-2E TCR beta chain	B	261	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class I histocompatibility antigen, A alpha chain	C [auth H]	276	Homo sapiens	Mutation(s): 3 Gene Names: HLA-A, HLAA
UniProt & NIH Common Fund Data Resources
Find proteins for P04439 (Homo sapiens) Go to UniProtKB: P04439
PHAROS: P04439 GTEx: ENSG00000206503
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04439-2
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	D [auth L]	100	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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61769
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylosuccinate synthetase	E [auth P]	9	Clostridium novyi NT	Mutation(s): 0 Gene Names: purA, NT01CX_0905 EC: 6.3.4.4
UniProt
Find proteins for A0PXA8 (Clostridium novyi (strain NT)) Explore A0PXA8 Go to UniProtKB: A0PXA8
Entity Groups
UniProt Group	A0PXA8
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.297 (Depositor), 0.296 (DCC)
R-Value Work: 0.240 (Depositor), 0.238 (DCC)
R-Value Observed: 0.242 (Depositor)

Space Group: P 6₂ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.095	α = 90
b = 119.095	β = 90
c = 313.054	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFC2302900
Chinese Academy of Sciences	China	YSBR-083
National Natural Science Foundation of China (NSFC)	China	32222031