4E41

Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4

• PDB DOI: https://doi.org/10.2210/pdb4E41/pdb

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


• Deposited: 2012-03-11 Released: 2012-08-29 
• Deposition Author(s): Deng, L., Langley, R.J., Wang, Q., Topalian, S.L., Mariuzza, R.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.264 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 

Starting Model: experimental

Literature

Structural basis for the recognition of mutant self by a tumor-specific, MHC class II-restricted T cell receptor G4

Deng, L., Langley, R.J., Wang, Q., Topalian, S.L., Mariuzza, R.A.

(2012) Proc Natl Acad Sci U S A 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 189.13 kDa 
• Atom Count: 12,983 
• Modelled Residue Count: 1,589 
• Deposited Residue Count: 1,658 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DR alpha chain	A, F	182	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRA, HLA-DRA1
UniProt & NIH Common Fund Data Resources
Find proteins for P01903 (Homo sapiens) Explore P01903  Go to UniProtKB:  P01903
PHAROS:  P01903 GTEx:  ENSG00000204287

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HLA class II histocompatibility antigen, DRB1-1 beta chain	B, G	190	Homo sapiens	Mutation(s): 0  Gene Names: HLA-DRB1
UniProt & NIH Common Fund Data Resources
Find proteins for P01911 (Homo sapiens) Explore P01911  Go to UniProtKB:  P01911
PHAROS:  P01911 GTEx:  ENSG00000196126

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	C, H	15	Homo sapiens	Mutation(s): 0  Gene Names: TPI1, TPI EC: 5.3.1.1 (PDB Primary Data), 4.2.3.3 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P60174 (Homo sapiens) Explore P60174  Go to UniProtKB:  P60174
PHAROS:  P60174 GTEx:  ENSG00000111669

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor G4 alpha chain	D, I	203	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor G4 beta chain	E, J	239	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	K [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.264 
• R-Value Work: 0.197 
• R-Value Observed: 0.201 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.133	α = 90
b = 175.611	β = 110.75
c = 88.646	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-29 
Deposition Author(s): Deng, L., Langley, R.J., Wang, Q., Topalian, S.L., Mariuzza, R.A.

Revision History  

• Version 1.0: 2012-08-29
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary