4E42 | pdb_00004e42

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/pdb4E42/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: 2.70 Å
R-Value Free:
0.263 (Depositor), 0.260 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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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: 100.14 kDa
Atom Count: 6,845
Modeled Residue Count: 829
Deposited Residue Count: 884
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor G4 alpha chain	A, C	203	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor G4 beta chain	B, D	239	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain F [auth B] MOL2 format, chain L [auth D] MOL2 format, chain F [auth B] mmCIF format, chain L [auth D] mmCIF format, chain F [auth B]	F [auth B], L [auth D]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain L [auth D] Interactions & Density Focus chain F [auth B] Focus chain L [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain J [auth B] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain I [auth B] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth B] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth B] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B]	E [auth A] G [auth B] H [auth B] I [auth B] J [auth B] E [auth A], G [auth B], H [auth B], I [auth B], J [auth B], M [auth D], N [auth D], O [auth D], P [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth D] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain K [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain K [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain K [auth B]	K [auth B], Q [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Focus chain Q [auth D] Interactions & Density Focus chain K [auth B] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.263 (Depositor), 0.260 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 168.07	α = 90
b = 75.365	β = 123.48
c = 130.859	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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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: 2024-11-06
Changes: Structure summary