7RJL

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

• PDB DOI: https://doi.org/10.2210/pdb7RJL/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: 1.50 Å
• R-Value Free: 0.185 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

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: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 31.28 kDa 
• Atom Count: 2,324 
• Modelled Residue Count: 243 
• Deposited Residue Count: 258 
• 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
Serine hydroxymethyltransferase, cytosolic	C, D	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	K [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], L [auth B], M [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: 1.50 Å
• R-Value Free: 0.185 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.55	α = 90
b = 61.572	β = 90
c = 83.634	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
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 2.0: 2023-11-15
  Changes: Atomic model, Data collection