3ROO

Murine class I major histocompatibility complex H-2Kb in complex with immunodominant LCMV-derived gp34-41 peptide

• PDB DOI: https://doi.org/10.2210/pdb3ROO/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Mammarenavirus choriomeningitidis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-04-26 Released: 2012-04-04 
• Deposition Author(s): Madhurantakam, C., Duru, A.D., Leong, C., Sandalova, T., Webb, J.R., Achour, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Starting Model: experimental

Literature

Nitro-tyrosination of the immunodominant LCMV epitope gp34-41 alters both its capacity to stabilize H-2Kb and the molecular surface of the MHC complex, affecting TCR recognition

Madhurantakam, C., Duru, A.D., Leong, C., Sandalova, T., Webb, J.R., Achour, A.

(2012) PLoS One 

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)

Macromolecule Content

• Total Structure Weight: 89.41 kDa 
• Atom Count: 6,694 
• Modelled Residue Count: 760 
• Deposited Residue Count: 764 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, K-B alpha chain	A, C	275	Mus musculus	Mutation(s): 0  Gene Names: H2-K1
UniProt
Find proteins for P01901 (Mus musculus) Explore P01901  Go to UniProtKB:  P01901

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, D	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
Pre-glycoprotein polyprotein GP complex	E, F	8	Mammarenavirus choriomeningitidis	Mutation(s): 0
UniProt
Find proteins for P07399 (Lymphocytic choriomeningitis virus (strain WE)) Explore P07399  Go to UniProtKB:  P07399

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MPD	H [auth B], J [auth C]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	I [auth B], K [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	G [auth A], L [auth D]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.267 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.448	α = 90
b = 92.588	β = 90
c = 128.827	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-04 
Deposition Author(s): Madhurantakam, C., Duru, A.D., Leong, C., Sandalova, T., Webb, J.R., Achour, A.

Revision History  

• Version 1.0: 2012-04-04
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2024-11-20
  Changes: Structure summary