9BD3

Structure of the MAGEA4 MHD-RAD18 R6BD Complex

PDB DOI: https://doi.org/10.2210/pdb9BD3/pdb

Classification: CELL CYCLE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-04-10 Released: 2024-06-05
Deposition Author(s): Forker, K., Zhou, P.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.226
R-Value Work: 0.191
R-Value Observed: 0.193

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of MAGEA4 MHD-RAD18 R6BD reveals a flipped binding mode compared to AlphaFold2 prediction.

Forker, K., Fleming, M.C., Pearce, K.H., Vaziri, C., Bowers, A.A., Zhou, P.

(2024) EMBO J 43: 2835-2839

PubMed: 38907034 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s44318-024-00140-2
Primary Citation of Related Structures:
9BD3

Organizational Affiliation

Department of Biochemistry, Duke University School of Medicine, Durham, NC, 27710, USA.

Macromolecule Content

Total Structure Weight: 56.71 kDa
Atom Count: 3,756
Modelled Residue Count: 462
Deposited Residue Count: 496
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Melanoma antigen A 4	A, C	220	Homo sapiens	Mutation(s): 0 Gene Names: MAGEA4
UniProt & NIH Common Fund Data Resources
Find proteins for P43358 (Homo sapiens) Explore P43358 Go to UniProtKB: P43358
PHAROS: P43358 GTEx: ENSG00000147381
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43358
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RAD18	B, D	28	Homo sapiens	Mutation(s): 0 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NS91 (Homo sapiens) Explore Q9NS91 Go to UniProtKB: Q9NS91
PHAROS: Q9NS91 GTEx: ENSG00000070950
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9NS91
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.58 Å
R-Value Free: 0.226
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.21	α = 90
b = 85.21	β = 90
c = 206.08	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-06-05

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2024-06-05
Type: Initial release
Version 1.1: 2024-07-03
Changes: Database references
Version 1.2: 2024-07-24
Changes: Database references

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.