3MFF | pdb_00003mff

1F1E8hu TCR

PDB DOI: https://doi.org/10.2210/pdb3MFF/pdb

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

Deposited: 2010-04-02 Released: 2010-06-02
Deposition Author(s): van Boxel, G.I., Holmes, S., Fugger, L., Jones, E.Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.200 (Depositor), 0.248 (DCC)
R-Value Observed:
0.202 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

An alternative conformation of the T-cell receptor alpha constant region

van Boxel, G.I., Holmes, S., Fugger, L., Jones, E.Y.

(2010) J Mol Biology 400: 828-837

PubMed: 20630474 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1016/j.jmb.2010.05.053
Primary Citation Related Structures:
3MFF

PubMed Abstract:
Alphabeta T-cell receptors (TcRs) play a central role in cellular immune response. They are members of the Ig superfamily, with extracellular regions of the alpha and beta chains each comprising a V-type domain and a C-type domain. We have determined the ectodomain structure of an alphabeta TcR, which recognizes the autoantigen myelin basic protein. The 2.0-A-resolution structure reveals canonical main-chain conformations for the V(alpha), V(beta), and C(beta) domains, but the C(alpha) domain exhibits a main-chain conformation remarkably different from those previously reported for TcR crystal structures. The global IgC-like fold is maintained, but a piston-like rearrangement between BC and DE beta-turns results in beta-strand slippage. This substantial conformational change may represent a signaling intermediate. Our structure is the first example for the Ig fold of the increasingly recognized concept of "metamorphic proteins."

Organizational Affiliation

Division of Structural Biology, Wellcome Trust Centre for Human Genetics, The University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecule Content

Total Structure Weight: 100.55 kDa
Atom Count: 7,784
Modeled Residue Count: 873
Deposited Residue Count: 884
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor alpha chain	A, C	200	Homo sapiens	Mutation(s): 0

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
T cell receptor beta chain	B, D	242	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARG Query on ARG Download:Ideal Coordinates CCD File SDF format, chain J [auth D] MOL2 format, chain J [auth D] mmCIF format, chain J [auth D]	J [auth D]	ARGININE C₆ H₁₅ N₄ O₂ ODKSFYDXXFIFQN-BYPYZUCNSA-O		Interactions Focus chain J [auth D] Interactions & Density Focus chain J [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth D] SDF format, chain E [auth A] MOL2 format, chain G [auth D] MOL2 format, chain E [auth A] mmCIF format, chain G [auth D] mmCIF format, chain E [auth A]	E [auth A], G [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth D]
URE Query on URE Download:Ideal Coordinates CCD File SDF format, chain I [auth D] SDF format, chain H [auth D] SDF format, chain F [auth B] MOL2 format, chain I [auth D] MOL2 format, chain H [auth D] MOL2 format, chain F [auth B] mmCIF format, chain I [auth D] mmCIF format, chain H [auth D] mmCIF format, chain F [auth B]	F [auth B], H [auth D], I [auth D]	UREA C H₄ N₂ O XSQUKJJJFZCRTK-UHFFFAOYSA-N		Interactions Focus chain F [auth B] Focus chain H [auth D] Focus chain I [auth D] Interactions & Density Focus chain F [auth B] Focus chain H [auth D] Focus chain I [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.200 (Depositor), 0.248 (DCC)
R-Value Observed: 0.202 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.323	α = 90
b = 74.016	β = 91.59
c = 94.267	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-06-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-06-02
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2014-03-05
Changes: Database references
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary