8FHU | pdb_00008fhu

Structure of Pyruvate dehydrogenase phosphatase regulatory subunit epitope presented by H2-Dd

• PDB DOI: https://doi.org/10.2210/pdb8FHU/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2022-12-15 Released: 2023-06-28 
• Deposition Author(s): Custodio, J.M.F., Baker, B.M.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 

Starting Model: experimental

Literature

Structure of Pyruvate dehydrogenase phosphatase regulatory subunit neoepitope presented by H2-Dd

Custodio, J.M.F., Baker, B.M.

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: native gel electrophoresis

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: 89.9 kDa 
• Atom Count: 6,327 
• Modeled Residue Count: 751 
• Deposited Residue Count: 770 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
H-2 class I histocompatibility antigen, D-D alpha chain	A, D	277	Mus musculus	Mutation(s): 0  Gene Names: H2-D1
UniProt
Find proteins for P01900 (Mus musculus) Explore P01900  Go to UniProtKB:  P01900

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B, E	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
Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial	C, F	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NCN5 (Homo sapiens) Explore Q8NCN5  Go to UniProtKB:  Q8NCN5
PHAROS:  Q8NCN5 GTEx:  ENSG00000090857

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K	G [auth A], H [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.415	α = 90
b = 104.564	β = 90
c = 169.993	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
BUCCANEER	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-28 
Deposition Author(s): Custodio, J.M.F., Baker, B.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118166

Revision History  

• Version 1.0: 2023-06-28
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary