3TBV

CRYSTAL STRUCTURE OF THE MURINE CLASS I MAJOR HISTOCOMPATIBILITY COMPLEX H-2DB IN COMPLEX WITH THE LCMV-DERIVED GP33 ALTERED PEPTIDE ligand (A2G,V3P,Y4A)

• PDB DOI: https://doi.org/10.2210/pdb3TBV/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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.278 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 179.95 kDa 
• Atom Count: 13,548 
• Modelled Residue Count: 1,536 
• Deposited Residue Count: 1,536 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-B alpha chain	A, C, E, G	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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D, F, H	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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein G1	I, J, K, L	9	Lymphocytic choriomeningitis virus (strain WE)	Mutation(s): 4
UniProt
Find proteins for P07399 (Lymphocytic choriomeningitis virus (strain WE)) Explore P07399  Go to UniProtKB:  P07399

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	M [auth A], Q [auth C], R [auth E], U [auth F]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	N [auth A], O [auth A], P [auth B], S [auth E], T [auth E], V [auth H], W [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.278 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.584	α = 90
b = 126.473	β = 106.71
c = 102.11	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 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.

Revision History  

• Version 1.0: 2012-08-08
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description