7RJP | pdb_00007rjp

Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with SHMT

• PDB DOI: https://doi.org/10.2210/pdb7RJP/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: 1.25 Å
• R-Value Free: 
  0.174 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.148 (Depositor), 0.154 (DCC) 
• R-Value Observed: 
  0.150 (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.

To be published.

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

Macromolecule Content 

• Total Structure Weight: 16.34 kDa 
• Atom Count: 1,400 
• Modeled Residue Count: 133 
• Deposited Residue Count: 133 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	127	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine hydroxymethyltransferase, cytosolic	B	6	Homo sapiens	Mutation(s): 0  EC: 2.1.2.1
UniProt & NIH Common Fund Data Resources
Find proteins for P34896 (Homo sapiens) Explore P34896  Go to UniProtKB:  P34896
PHAROS:  P34896 GTEx:  ENSG00000176974

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	O [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	L [auth A], M [auth A], N [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.174 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.148 (Depositor), 0.154 (DCC) 
• R-Value Observed: 0.150 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.043	α = 90
b = 51.56	β = 90
c = 57.384	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALEPACK	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: 2023-10-18
  Changes: Data collection, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection
• Version 2.1: 2024-10-30
  Changes: Structure summary