6G9R

Murine class I major histocompatibility complex H-2 Db in complex with self-antigen derived from dopamine monooxygenase.

• PDB DOI: https://doi.org/10.2210/pdb6G9R/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-04-11 Released: 2019-04-24 
• Deposition Author(s): Achour, A., Sandalova, T., Allerbring, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.264 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 

Starting Model: experimental

Literature

Structural basis for CD8+ T cells auto-reactivity in LCMV infection

Allerbring, E., Duru, A.D., Nygren, P.A., Sandalova, T., 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 Evidence: gel filtration

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: 179.32 kDa 
• Atom Count: 12,665 
• 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
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): 1  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
Dopamine beta-hydroxylase	I [auth P], J [auth I], K [auth J], L [auth K]	9	Mus musculus	Mutation(s): 1  EC: 1.14.17.1
UniProt
Find proteins for Q64237 (Mus musculus) Explore Q64237  Go to UniProtKB:  Q64237

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.264 
• R-Value Work: 0.234 
• R-Value Observed: 0.236 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.245	α = 90
b = 123.597	β = 103.07
c = 99.262	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Achour, A., Sandalova, T., Allerbring, E.

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary