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- PDB-7rjr: Crystal structure of human Bromodomain containing protein 4 (BRD4... -

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Basic information

Entry
Database: PDB / ID: 7rjr
TitleCrystal structure of human Bromodomain containing protein 4 (BRD4) in complex with BCLTF1
Components
  • Bcl-2-associated transcription factor 1
  • Bromodomain-containing protein 4
KeywordsSIGNALING PROTEIN / BRD4 / BCLTF1 / acetyllysine
Function / homology
Function and homology information


positive regulation of DNA-templated transcription initiation / mediator complex / RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / positive regulation of intrinsic apoptotic signaling pathway ...positive regulation of DNA-templated transcription initiation / mediator complex / RNA polymerase II C-terminal domain binding / P-TEFb complex binding / negative regulation of DNA damage checkpoint / histone H4 reader activity / host-mediated suppression of viral transcription / positive regulation of G2/M transition of mitotic cell cycle / positive regulation of T-helper 17 cell lineage commitment / positive regulation of intrinsic apoptotic signaling pathway / : / RNA polymerase II CTD heptapeptide repeat kinase activity / cellular response to leukemia inhibitory factor / 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 / nuclear speck / positive regulation of apoptotic process / chromatin remodeling / negative regulation of DNA-templated transcription / protein serine/threonine kinase activity / apoptotic process / 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 / DNA binding / RNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
THRAP3/BCLAF1 family / THRAP3/BCLAF1 family / 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 ...THRAP3/BCLAF1 family / THRAP3/BCLAF1 family / 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 / Bcl-2-associated transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 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: To Be Published
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 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 9, 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: Bcl-2-associated transcription factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4204
Polymers16,3352
Non-polymers852
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.321, 43.796, 78.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15099.380 Da / Num. of mol.: 1
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 Bcl-2-associated transcription factor 1 / Btf / BCLAF1 and THRAP3 family member 1


Mass: 1235.475 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 1.96 Å3/Da / Density % sol: 37.31 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% w/v PEG4000, 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 1, 2020
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.45→23.01 Å / Num. obs: 23219 / % possible obs: 99.5 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.029 / Rrim(I) all: 0.102 / Net I/σ(I): 15.7 / Num. measured all: 292317 / Scaling rejects: 1
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
1.45-1.489.50.602989210430.9330.1950.6343.391.1
7.97-23.0110.20.04417801750.9990.0130.04736.296.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MXF

3mxf


Resolution: 1.45→23.01 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 1150 4.97 %
Rwork0.1705 21997 -
obs0.1724 23147 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.05 Å2 / Biso mean: 17.5268 Å2 / Biso min: 7.18 Å2
Refinement stepCycle: final / Resolution: 1.45→23.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 5 138 1233
Biso mean--24.71 26.13 -
Num. residues----131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.520.221250.19232620274596
1.52-1.60.20991230.179227302853100
1.6-1.70.22961500.172527182868100
1.7-1.830.22031460.178827252871100
1.83-2.020.18931420.176427382880100
2.02-2.310.2061540.16927642918100
2.31-2.910.22331440.177227922936100
2.91-23.010.19681660.158229103076100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.24964.5618-2.88094.1192-1.53028.06220.1774-0.02520.43850.85210.0290.0889-0.5449-0.2401-0.23020.15670.0120.02940.1165-0.02940.1237-14.93710.56213.105
23.20883.18312.02057.3743-2.93158.14260.148-0.0191-0.10830.1802-0.33150.09680.08190.00810.11130.106-0.00590.02220.1422-0.01980.1091-13.04-4.57725.546
30.9656-1.18350.00353.0421-0.65621.3714-0.00140.03340.03120.0248-0.0229-0.12180.0460.070.03250.0594-0.0089-0.00050.0927-0.01050.0889-7.786-1.696.323
40.71-0.92630.57343.2197-2.3494.0077-0.0957-0.1209-0.05740.1130.1030.02760.00210.0160.02120.0766-0.00110.00920.0903-0.0140.0747-13.31-3.44415.029
50.7981-1.67251.88054.8712-3.84275.29760.0308-0.0067-0.06-0.02170.10880.14330.1123-0.1421-0.17730.0906-0.0097-0.00080.1108-0.00970.1072-17.537-2.8344.029
61.2019-0.0496-0.16586.3101-3.33715.527-0.020.0102-0.1598-0.13350.04930.07090.36190.02360.02150.0762-0.0182-0.00030.1084-0.02470.1228-11.779-10.7761.366
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 43:48 )A43 - 48
2X-RAY DIFFRACTION2( CHAIN A AND RESID 49:59 )A49 - 59
3X-RAY DIFFRACTION3( CHAIN A AND RESID 60:98 )A60 - 98
4X-RAY DIFFRACTION4( CHAIN A AND RESID 99:125 )A99 - 125
5X-RAY DIFFRACTION5( CHAIN A AND RESID 126:140 )A126 - 140
6X-RAY DIFFRACTION6( CHAIN A AND RESID 141:168 )A141 - 168

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