3QIU

Crystal structure of the 226 TCR in complex with MCC/I-Ek

PDB DOI: https://doi.org/10.2210/pdb3QIU/pdb

Classification: IMMUNE SYSTEM
Organism(s): Mus musculus, Manduca sexta
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): No

Deposited: 2011-01-27 Released: 2011-04-27
Deposition Author(s): Kruse, A.C., Ely, L.K., Newell, E.W., Davis, M.M., Garcia, K.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.254
R-Value Work: 0.215
R-Value Observed: 0.217

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 96.08 kDa
Atom Count: 6,379
Modelled Residue Count: 775
Deposited Residue Count: 836
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K alpha chain	A	179	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P04224 (Mus musculus) Explore P04224 Go to UniProtKB: P04224
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04224
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC CLASS II H2-IA-BETA CHAIN	B	196	Mus musculus	Mutation(s): 0 Gene Names: H2-Eb1
UniProt & NIH Common Fund Data Resources
Find proteins for P04230 (Mus musculus) Explore P04230 Go to UniProtKB: P04230
IMPC: MGI:95901
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04230
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR 226 alpha chain	C	205	Mus musculus	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
TCR 226 beta chain	D	243	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
MCC peptide	E	13	Manduca sexta	Mutation(s): 0
UniProt
Find proteins for P00039 (Manduca sexta) Explore P00039 Go to UniProtKB: P00039
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00039
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth B]	F [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.254
R-Value Work: 0.215
R-Value Observed: 0.217
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.79	α = 90
b = 71.4	β = 90.75
c = 106.07	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-04-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-04-27
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-08-10
Changes: Database references
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary