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- PDB-7rjn: Crystal structure of human bromodomain containing protein 3 (BRD3... -

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Basic information

Entry
Database: PDB / ID: 7rjn
TitleCrystal structure of human bromodomain containing protein 3 (BRD3) in complex with BCLTF1
Components
  • Bcl-2-associated transcription factor 1
  • Bromodomain-containing protein 3
KeywordsSIGNALING PROTEIN / BRD3 / BCL2TF / acetyllysine
Function / homology
Function and homology information


: / : / positive regulation of DNA-templated transcription initiation / mediator complex / lncRNA binding / endodermal cell differentiation / positive regulation of intrinsic apoptotic signaling pathway / protein localization to chromatin / molecular condensate scaffold activity / cellular response to leukemia inhibitory factor ...: / : / positive regulation of DNA-templated transcription initiation / mediator complex / lncRNA binding / endodermal cell differentiation / positive regulation of intrinsic apoptotic signaling pathway / protein localization to chromatin / molecular condensate scaffold activity / cellular response to leukemia inhibitory factor / transcription coregulator activity / lysine-acetylated histone binding / nuclear speck / chromatin remodeling / positive regulation of apoptotic process / negative regulation of DNA-templated transcription / apoptotic process / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Bcl-2-associated transcription factor 1 / THRAP3/BCLAF1 family / THRAP3/BCLAF1 family / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site ...Bcl-2-associated transcription factor 1 / THRAP3/BCLAF1 family / THRAP3/BCLAF1 family / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II / Brdt, bromodomain, repeat I / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 3 / Bcl-2-associated transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsFedorov, E. / Islam, K. / Ghosh, A.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM123234 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130752 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P01GM118303 United States
CitationJournal: Biorxiv / Year: 2021
Title: Uncovering the Bromodomain Interactome using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization
Authors: Wagner, S. / Fedorov, E. / Sudhamalla, B. / Jnawali, H.N. / Debiec, R. / Ghosh, A. / Islam, K.
History
DepositionJul 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 3
B: Bromodomain-containing protein 3
C: Bcl-2-associated transcription factor 1
D: Bcl-2-associated transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8317
Polymers31,6454
Non-polymers1863
Water2,504139
1
A: Bromodomain-containing protein 3
C: Bcl-2-associated transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8843
Polymers15,8222
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-4 kcal/mol
Surface area7310 Å2
MethodPISA
2
B: Bromodomain-containing protein 3
D: Bcl-2-associated transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,9464
Polymers15,8222
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint0 kcal/mol
Surface area7240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.729, 54.793, 122.242
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Bromodomain-containing protein 3 / RING3-like protein


Mass: 14586.843 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD3, KIAA0043, RING3L / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: Q15059
#2: Protein/peptide Bcl-2-associated transcription factor 1 / Btf / BCLAF1 and THRAP3 family member 1


Mass: 1235.475 Da / Num. of mol.: 2 / Fragment: UNP residues 330-339 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NYF8
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium acetate, 0.1 M sodium acetate trihydrate, 30% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 31, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.95→29.49 Å / Num. obs: 21679 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.038 / Rrim(I) all: 0.139 / Net I/σ(I): 14.3 / Num. measured all: 285809 / Scaling rejects: 350
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.95-213.90.6782045714720.9480.1880.7034.699.9
8.94-29.4911.20.07130232690.9970.0240.0752397.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6QJU

6qju


Resolution: 1.95→20 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.234 -5.01 %
Rwork0.183 --
obs0.1852 21592 99.7 %
Displacement parametersBiso mean: 25.4 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2079 0 12 139 2230
LS refinement shellResolution: 1.95→2.02 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2496 98 -
Rwork0.2016 2010 -
obs--100 %

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