3TBS

CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX THE WITH LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (V3P,Y4A)

PDB DOI: https://doi.org/10.2210/pdb3TBS/pdb

Classification: Immune system/agonist
Organism(s): Mus musculus, Lymphocytic choriomeningitis virus (strain WE)
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2011-08-08 Released: 2012-08-08
Deposition Author(s): Duru, A.D., Allerbring, E.B., Uchtenhagen, H., Mazumdar, P.A., Badia-Martinez, D., Madhurantakam, C., Sandalova, T., Nygren, P., Achour, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.270
R-Value Work: 0.230
R-Value Observed: 0.232

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Conversion of a T cell viral antagonist into an agonist through higher stabilization and conserved molecular mimicry: Implications for TCR recognition

Duru, A.D., Allerbring, E.B., Uchtenhagen, H., Mazumdar, P.A., Badia-Martinez, D., Madhurantakam, C., Sandalova, T., Nygren, P., Achour, A.

To be published.

Macromolecule Content

Total Structure Weight: 89.86 kDa
Atom Count: 6,389
Modelled Residue Count: 759
Deposited Residue Count: 768
Unique protein chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-B alpha chain	A, D	276	Mus musculus	Mutation(s): 0 Gene Names: H2-D1, H2-DB
UniProt
Find proteins for P01899 (Mus musculus) Explore P01899 Go to UniProtKB: P01899
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01899
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	99	Mus musculus	Mutation(s): 0 Gene Names: B2m
UniProt & NIH Common Fund Data Resources
Find proteins for P01887 (Mus musculus) Explore P01887 Go to UniProtKB: P01887
IMPC: MGI:88127
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOPROTEIN G1	C, F	9	Lymphocytic choriomeningitis virus (strain WE)	Mutation(s): 3
UniProt
Find proteins for P07399 (Lymphocytic choriomeningitis virus (strain WE)) Explore P07399 Go to UniProtKB: P07399
Entity Groups
UniProt Group	P07399
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth D]	G [auth A], I [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain I [auth D] Interactions & Density Focus chain G [auth A] Focus chain I [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain J [auth D] MOL2 format, chain H [auth A] MOL2 format, chain J [auth D] mmCIF format, chain H [auth A] mmCIF format, chain J [auth D]	H [auth A], J [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain J [auth D] Interactions & Density Focus chain H [auth A] Focus chain J [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.49 Å
R-Value Free: 0.270
R-Value Work: 0.230
R-Value Observed: 0.232
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.84	α = 90
b = 125.12	β = 128.15
c = 101.32	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2012-08-08

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-08-08
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-27
Changes: Structure summary