9K2I | pdb_00009k2i

Rac1 epitope specific TCR 5934 binding to Rac1P29S-HLA-A2

• PDB DOI: https://doi.org/10.2210/pdb9K2I/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-10-17 Released: 2025-10-22 
• Deposition Author(s): Yang, D.D., Wu, D.C.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free: 
  0.290 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Models: experimental

Literature

Rac1 epitope specific TCR 5934 binding to Rac1P29S-HLA-A2

Yang, D.D., Wu, D.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: surface plasmon resonance

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 383.5 kDa 
• Atom Count: 26,756 
• Modeled Residue Count: 3,316 
• Deposited Residue Count: 3,356 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I antigen	A, D [auth F], H [auth K], K [auth P]	276	Homo sapiens	Mutation(s): 0  Gene Names: HLA-A
UniProt
Find proteins for Q8WLS4 (Homo sapiens) Explore Q8WLS4  Go to UniProtKB:  Q8WLS4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E [auth G], I [auth L], L [auth Q]	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PHE-SER-GLY-GLU-TYR-ILE-PRO-THR-VAL	C, F [auth H], J [auth M], M [auth R]	9	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor 5934 chain beta	G [auth J], P [auth E], R [auth T], T [auth O]	247	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor5934 chain alpha	N [auth I], O [auth D], Q [auth S], S [auth N]	207	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.05 Å
• R-Value Free:  0.290 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.303	α = 90
b = 147.504	β = 94.25
c = 122.171	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-22 
Deposition Author(s): Yang, D.D., Wu, D.C.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32270995
National Natural Science Foundation of China (NSFC)	China	32100985

Revision History  

• Version 1.0: 2025-10-22
  Type: Initial release