7RJK | pdb_00007rjk

Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with hnRNPK

• PDB DOI: https://doi.org/10.2210/pdb7RJK/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-21 Released: 2022-08-03 
• Deposition Author(s): Fedorov, E., Islam, K., Ghosh, A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.217 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Uncovering the Bromodomain Interactome using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization

Wagner, S., Fedorov, E., Sudhamalla, B., Jnawali, H.N., Debiec, R., Ghosh, A., Islam, K.

(2021) bioRxiv 

• DOI: https://doi.org/10.1101/2021.07.28.453719

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 31.84 kDa 
• Atom Count: 2,486 
• Modeled Residue Count: 260 
• Deposited Residue Count: 266 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 3	A, B	123	Homo sapiens	Mutation(s): 0  Gene Names: BRD3, KIAA0043, RING3L
UniProt & NIH Common Fund Data Resources
Find proteins for Q15059 (Homo sapiens) Explore Q15059  Go to UniProtKB:  Q15059
PHAROS:  Q15059 GTEx:  ENSG00000169925

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heterogeneous nuclear ribonucleoprotein K	C, D	10	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61978 (Homo sapiens) Explore P61978  Go to UniProtKB:  P61978
PHAROS:  P61978 GTEx:  ENSG00000165119

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	G [auth B], H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	C, D	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.217 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.658	α = 90
b = 49.658	β = 90
c = 255.611	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-08-03 
Deposition Author(s): Fedorov, E., Islam, K., Ghosh, A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM123234
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM130752
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01GM118303

Revision History  

• Version 1.0: 2022-08-03
  Type: Initial release
  
• Version 1.1: 2022-08-24
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-11-06
  Changes: Structure summary