9BD3 | pdb_00009bd3

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 (Depositor), 0.226 (DCC)
R-Value Work:
0.191 (Depositor), 0.191 (DCC)
R-Value Observed:
0.193 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s44318-024-00140-2
Primary Citation 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
Modeled Residue Count: 462
Deposited Residue Count: 496
Unique protein chains: 2

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43358
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Depositor), 0.226 (DCC)
R-Value Work: 0.191 (Depositor), 0.191 (DCC)
R-Value Observed: 0.193 (Depositor)

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

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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

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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.