3ROL

Murine class I major histocompatibility complex H-2Kb in complex with post-translationally modified LCMV-derived gp34-41 peptide, comprising a nitrotyrosine at position 3

• PDB DOI: https://doi.org/10.2210/pdb3ROL/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: 2.60 Å
• R-Value Free: 0.295 
• R-Value Work: 0.246 
• R-Value Observed: 0.249 

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: 89.29 kDa 
• Atom Count: 6,447 
• Modelled Residue Count: 757 
• 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: H-2Kb, H2-K, 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): 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
Pre-glycoprotein polyprotein GP complex	E, F	8	Mammarenavirus choriomeningitidis	Mutation(s): 1
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	J [auth D]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4	G [auth A], I [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL	H [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NIY	E, F	L-PEPTIDE LINKING	C9 H10 N2 O5		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.295 
• R-Value Work: 0.246 
• R-Value Observed: 0.249 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.466	α = 90
b = 88.496	β = 94.71
c = 119.05	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	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