3MUK | pdb_00003muk

Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23

• PDB DOI: https://doi.org/10.2210/pdb3MUK/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-03 Released: 2010-08-11 
• Deposition Author(s): Vollmuth, F., Geyer, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Interaction of propionylated and butyrylated histone H3 lysine marks with Brd4 bromodomains

Vollmuth, F., Geyer, M.

(2010) Angew Chem Int Ed Engl 49: 6768-6772

• PubMed: 20715035 
• DOI: https://doi.org/10.1002/anie.201002724
• Primary Citation of Related Structures:  
  3MUK, 3MUL

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Organizational Affiliation: 

Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.34 kDa 
• Atom Count: 1,230 
• Modelled Residue Count: 134 
• Deposited Residue Count: 139 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	131	Mus musculus	Mutation(s): 0  Gene Names: Brd4, Mcap
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ESU6 (Mus musculus) Explore Q9ESU6  Go to UniProtKB:  Q9ESU6
IMPC:  MGI:1888520

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
peptide of Histone H3.3	B [auth D]	8	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243 GTEx:  ENSG00000132475 ENSG00000163041

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PRK	B [auth D]	L-PEPTIDE LINKING	C9 H18 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.213	α = 90
b = 47.008	β = 90
c = 78.101	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-08-11 
Deposition Author(s): Vollmuth, F., Geyer, M.

Revision History  

• Version 1.0: 2010-08-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description