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- PDB-7tv0: Crystal structure of BRD4 bromodomain 1 in complex with dual-acet... -

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Basic information

Entry
Database: PDB / ID: 7tv0
TitleCrystal structure of BRD4 bromodomain 1 in complex with dual-acetylated SARS-CoV-2 E
Components
  • Bromodomain-containing protein 4
  • Envelope small membrane protein
KeywordsTRANSCRIPTION / BRD4 / bromodomain / SARS-CoV-2 / COVID / envelope protein / E protein
Function / homology
Function and homology information


histone H4K8ac reader activity / histone H3K9ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription ...histone H4K8ac reader activity / histone H3K9ac reader activity / RNA polymerase II C-terminal domain binding / histone H3K27ac reader activity / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / histone H4K5ac reader activity / histone H4K12ac reader activity / host-mediated suppression of viral transcription / histone H4K16ac reader activity / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / p53 binding / chromosome / regulation of inflammatory response / histone binding / Potential therapeutics for SARS / transcription coactivator activity / positive regulation of canonical NF-kappaB signal transduction / transcription cis-regulatory region binding / chromatin remodeling / protein serine/threonine kinase activity / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus
Similarity search - Function
Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site ...Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II / NET domain superfamily / NET domain profile. / : / NET domain / Bromodomain extra-terminal - transcription regulation / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Severe acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsVann, K.R. / Holt, T.A. / 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
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Bromodomain-containing protein 4
C: Bromodomain-containing protein 4
D: Bromodomain-containing protein 4
E: Envelope small membrane protein
G: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)68,5696
Polymers68,5696
Non-polymers00
Water4,288238
1
A: Bromodomain-containing protein 4
G: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)17,9292
Polymers17,9292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-9 kcal/mol
Surface area8630 Å2
MethodPISA
2
B: Bromodomain-containing protein 4
E: Envelope small membrane protein


Theoretical massNumber of molelcules
Total (without water)17,9292
Polymers17,9292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-10 kcal/mol
Surface area8790 Å2
MethodPISA
3
C: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)16,3561
Polymers16,3561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8130 Å2
MethodPISA
4
D: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)16,3561
Polymers16,3561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.320, 96.220, 78.950
Angle α, β, γ (deg.)90.000, 94.370, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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


Mass: 16355.832 Da / Num. of mol.: 4 / 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


Mass: 1572.783 Da / Num. of mol.: 2 / Fragment: UNP residues 53-64 / Source method: obtained synthetically / Details: synthetic peptide acetylated at K53 and K63
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 54.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 1.5 M ammonium sulfate, 0.1 mM 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: Jan 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→48.1 Å / Num. obs: 24678 / % possible obs: 96.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 22.12 Å2 / CC1/2: 0.974 / Rmerge(I) obs: 0.159 / Rpim(I) all: 0.116 / Rrim(I) all: 0.198 / Net I/σ(I): 5.6 / Num. measured all: 66996 / Scaling rejects: 69
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
2.5-2.620.867500625460.3920.7221.1351.289.3
9.01-48.12.50.06113135300.9890.0460.07712.393.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.25 Å48.11 Å
Translation3.25 Å48.11 Å

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
PHASER2.8.3phasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3UVW

3uvw


Resolution: 2.6→34.39 Å / SU ML: 0.3671 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.7033
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2922 1911 8.92 %
Rwork0.2428 19502 -
obs0.2472 21413 94.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.34 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4717 0 0 238 4955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00394888
X-RAY DIFFRACTIONf_angle_d0.72966650
X-RAY DIFFRACTIONf_chiral_restr0.0571716
X-RAY DIFFRACTIONf_plane_restr0.0045860
X-RAY DIFFRACTIONf_dihedral_angle_d14.1957633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.670.4181150.3351252X-RAY DIFFRACTION86.3
2.67-2.740.41171490.28291362X-RAY DIFFRACTION92.47
2.74-2.820.27691340.27981341X-RAY DIFFRACTION92.01
2.82-2.910.32631190.26781419X-RAY DIFFRACTION93.72
2.91-3.010.32921460.2581364X-RAY DIFFRACTION95.09
3.01-3.130.31141380.26651395X-RAY DIFFRACTION95.57
3.13-3.280.29881300.25631443X-RAY DIFFRACTION96.8
3.28-3.450.3271430.25961433X-RAY DIFFRACTION96.75
3.45-3.660.31361410.2441360X-RAY DIFFRACTION94.17
3.66-3.950.26551400.21731415X-RAY DIFFRACTION95.87
3.95-4.340.25391280.21691394X-RAY DIFFRACTION93.78
4.34-4.970.2371310.2051412X-RAY DIFFRACTION93.86
4.97-6.250.26551510.22681439X-RAY DIFFRACTION97.43
6.26-34.390.24271460.22121473X-RAY DIFFRACTION97.71

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