6A8R

Crystal structure of DUX4 HD2 domain associated with ERG DNA binding site

PDB DOI: https://doi.org/10.2210/pdb6A8R/pdb
NAKB: 6A8R

Classification: DNA BINDING PROTEIN/DNA
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-07-10 Released: 2018-10-24
Deposition Author(s): Dong, X., Zhang, H., Cheng, N., Meng, G.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.207
R-Value Work: 0.201
R-Value Observed: 0.201

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

DUX4HD2-DNAERGstructure reveals new insight into DUX4-Responsive-Element.

Dong, X., Zhang, H., Cheng, N., Li, K., Meng, G.

(2019) Leukemia 33: 550-553

PubMed: 30315230 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41375-018-0273-z
Primary Citation of Related Structures:
6A8R

Organizational Affiliation

State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital, Shanghai JiaoTong University School of Medicine and School of Life Sciences and Biotechnology, Shanghai JiaoTong University, 197 Ruijin Er Road, Shanghai, 200025, China.

Macromolecule Content

Total Structure Weight: 20.45 kDa
Atom Count: 1,492
Modelled Residue Count: 136
Deposited Residue Count: 142
Unique protein chains: 1
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Double homeobox protein 4	A [auth B], B [auth A]	60	Homo sapiens	Mutation(s): 0 Gene Names: DUX4, DUX10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBX2 (Homo sapiens) Explore Q9UBX2 Go to UniProtKB: Q9UBX2
PHAROS: Q9UBX2 GTEx: ENSG00000260596
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UBX2
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PTPGPAPTPGPAPGPAPTPT)-3')	C [auth E]	11	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(PAPAPTPCPTPCPAPTPCPA)-3')	D [auth F]	11	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.207
R-Value Work: 0.201
R-Value Observed: 0.201
Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.55	α = 90
b = 32.55	β = 90
c = 126.591	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-24

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	81770142

Revision History (Full details and data files)

Version 1.0: 2018-10-24
Type: Initial release
Version 1.1: 2018-11-07
Changes: Data collection, Database references
Version 1.2: 2019-02-20
Changes: Data collection, Database references
Version 1.3: 2023-11-22
Changes: Data collection, Database references, Refinement description