6MP0

Crystal structures of the murine class I major histocompatibility complex H-2Db in complex with the TRP1-M9 peptide

• PDB DOI: https://doi.org/10.2210/pdb6MP0/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2018-10-05 Released: 2018-11-07 
• Deposition Author(s): Clancy-Thompson, E., Devlin, C.A., Birnbaum, M.E., Dougan, S.K.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 50.5 kDa 
• Atom Count: 3,580 
• Modelled Residue Count: 388 
• Deposited Residue Count: 447 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRP1-M9 peptide, Beta-2-microglobulin,H-2 class I histocompatibility antigen, D-B alpha chain, chimeric construct	A	447	Mus musculus	Mutation(s): 2  Gene Names: Tyrp1, Tyrp-1, B2m, H2-D1 EC: 1.14.18
UniProt & NIH Common Fund Data Resources
Find proteins for P01899 (Mus musculus) Explore P01899  Go to UniProtKB:  P01899
Find proteins for P01887 (Mus musculus) Explore P01887  Go to UniProtKB:  P01887
IMPC:  MGI:88127
Find proteins for P07147 (Mus musculus) Explore P07147  Go to UniProtKB:  P07147
UniProt Groups	P01899P01887P07147

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.061	α = 90
b = 98.436	β = 90
c = 121.772	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Currently 6MP0 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2018-11-07 
Deposition Author(s): Clancy-Thompson, E., Devlin, C.A., Birnbaum, M.E., Dougan, S.K.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	P30-CA14051
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	T32CA207021

Revision History  

• Version 1.0: 2018-11-07
  Type: Initial release
  
• Version 1.1: 2018-11-28
  Changes: Data collection, Database references
• Version 1.2: 2018-12-12
  Changes: Data collection, Database references
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-10-11
  Changes: Data collection, Database references, Refinement description, Structure summary