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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.230 (Depositor), 0.244 (DCC)
R-Value Work:
0.186 (Depositor), 0.196 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8D5J

This is version 1.2 of the entry. See complete history.

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.

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

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01902
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01887
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
UniProt Group	Q99KP6
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.230 (Depositor), 0.244 (DCC)
R-Value Work: 0.186 (Depositor), 0.196 (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

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-06

Deposition Author(s):

Custodio, J.M.F.

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

Revision History (Full details and data files)

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

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.