8D5J | pdb_00008d5j

The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd

• PDB DOI: https://doi.org/10.2210/pdb8D5J/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-06-04 Released: 2022-07-06 
• 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: 1.95 Å
• R-Value Free: 
  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.200 (DCC) 

Starting Model: experimental

Literature

The complex of Pre-mRNA-Processing Factor 19 (Prpf19) neoantigen KYLQVASHV Presented by H2-Kd

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: gel filtration

Macromolecule Content 

• Total Structure Weight: 45.13 kDa 
• Atom Count: 3,274 
• Modeled Residue Count: 384 
• Deposited Residue Count: 385 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MHC class I heavy chain maturation peptide H-2K(D)	A	276	Mus musculus	Mutation(s): 0  Gene Names: H2-K1
UniProt
Find proteins for P01902 (Mus musculus) Explore P01902  Go to UniProtKB:  P01902

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-2-microglobulin	B	100	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-mRNA-processing factor 19	C	9	Mus musculus	Mutation(s): 0  EC: 2.3.2.27
UniProt
Find proteins for Q99KP6 (Mus musculus) Explore Q99KP6  Go to UniProtKB:  Q99KP6

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.230 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.200 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.44	α = 90
b = 66.57	β = 92.01
c = 56.96	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
SCALEPACK	data scaling
PHASER	phasing
BUCCANEER	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-06 
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: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary