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- PDB-7tuq: Crystal structure of BRD4 bromodomain 1 in complex with monoacety... -

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Basic information

Entry
Database: PDB / ID: 7tuq
TitleCrystal structure of BRD4 bromodomain 1 in complex with monoacetylated SARS-CoV-2 E
Components
  • Bromodomain-containing protein 4BRD4
  • Envelope small membrane protein
KeywordsTRANSCRIPTION / BRD4 / bromodomain / SARS-CoV-2 / COVID / envelope protein / E protein
Function / homology
Function and homology information


viral budding from Golgi membrane / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / cytoplasmic capsid assembly / Regulation of gap junction activity / host cell Golgi membrane / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / endoplasmic reticulum-Golgi intermediate compartment ...viral budding from Golgi membrane / Tight junction interactions / SARS-CoV-2 targets PDZ proteins in cell-cell junction / cytoplasmic capsid assembly / Regulation of gap junction activity / host cell Golgi membrane / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / endoplasmic reticulum-Golgi intermediate compartment / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / Maturation of protein E / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / : / p53 binding / monoatomic ion channel activity / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Translation of Structural Proteins / Virion Assembly and Release / Induction of Cell-Cell Fusion / structural constituent of virion / Potential therapeutics for SARS / Attachment and Entry / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / SARS-CoV-2 activates/modulates innate and adaptive immune responses / virion membrane / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / membrane / identical protein binding / nucleus
Similarity search - Function
Envelope small membrane protein, SARS-CoV-2-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily / NET domain profile. / Brdt, bromodomain, repeat II ...Envelope small membrane protein, SARS-CoV-2-like / Envelope small membrane protein, coronavirus / Envelope small membrane protein, betacoronavirus / Coronavirus small envelope protein E / Coronavirus envelope (CoV E) protein profile. / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / 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 4 / Envelope small membrane protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.68 Å
AuthorsVann, K.R. / Kutateladze, T.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2022
Title: Binding of the SARS-CoV-2 envelope E protein to human BRD4 is essential for infection.
Authors: Vann, K.R. / Acharya, A. / Jang, S.M. / Lachance, C. / Zandian, M. / Holt, T.A. / Smith, A.L. / Pandey, K. / Durden, D.L. / El-Gamal, D. / Cote, J. / Byrareddy, S.N. / Kutateladze, T.G.
History
DepositionFeb 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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 4
B: Bromodomain-containing protein 4
C: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)33,8733
Polymers33,8733
Non-polymers00
Water1,09961
1
A: Bromodomain-containing protein 4
C: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)17,4602
Polymers17,4602
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area7620 Å2
MethodPISA
2
B: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)16,4131
Polymers16,4131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.463, 91.392, 100.268
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Bromodomain-containing protein 4 / BRD4 / Protein HUNK1


Mass: 16412.885 Da / Num. of mol.: 2 / Fragment: BD1 (UNP residues 42-180)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60885
#2: Protein/peptide Envelope small membrane protein / E / sM protein


Mass: 1047.145 Da / Num. of mol.: 1 / Fragment: UNP residues 60-68 / Source method: obtained synthetically / Details: synthetic peptide acetylated at K63
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: UniProt: P0DTC4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.5 M ammonium sulfate, 0.1 M Tris, pH 8.5, 12% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.68→41.58 Å / Num. obs: 10335 / % possible obs: 96.4 % / Redundancy: 2.637 % / Biso Wilson estimate: 31.216 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.105 / Χ2: 1.114 / Net I/σ(I): 11.58 / Num. measured all: 49987
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.68-2.842.4140.2422.7269113187286310.30989.8
2.84-3.032.7180.2564.067978297329350.9130.31898.7
3.03-3.282.7090.1715.847172277226470.9960.21595.5
3.28-3.592.7360.1099.236865254925090.9840.13698.4
3.59-42.6760.06515.836071231522690.9920.08298
4-4.622.680.04421.885359204320000.9960.05597.9
4.62-5.642.6810.04320.244494171016760.9970.05398
5.64-7.92.5660.04618.923380134713170.9970.05797.8
7.9-41.582.3840.02430.817577657370.9990.0396.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å41.58 Å
Translation3.5 Å41.58 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3JVK

3jvk


Resolution: 2.68→41.58 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 28.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.276 1001 9.98 %
Rwork0.216 9026 -
obs0.222 10027 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.91 Å2 / Biso mean: 40.891 Å2 / Biso min: 7.47 Å2
Refinement stepCycle: final / Resolution: 2.68→41.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 27 61 2048
Biso mean--74.85 33.69 -
Num. residues----230
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.68-2.820.3811280.3381114787
2.82-2.990.29371320.2643123192
2.99-3.230.28621430.2267128397
3.23-3.550.32461460.2161130697
3.55-4.060.24831460.1734131799
4.06-5.120.24111500.1718134299
5.12-41.580.25811560.2358140099

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