4E41 | pdb_00004e41

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.264 (Depositor), 0.248 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01903
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01911
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60174
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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

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| 3D Structure

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	3D Interactions
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain K [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A]	K [auth A], L [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth B] Interactions & Density Focus chain K [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.264 (Depositor), 0.248 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.201 (Depositor)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-08-29

Deposition Author(s):

Revision History (Full details and data files)

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