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

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Basic information

Entry
Database: PDB / ID: 7rjo
TitleCrystal structure of human Bromodomain containing protein 4 (BRD4) in complex with hnRNPK
Components
  • Bromodomain-containing protein 4
  • Heterogeneous nuclear ribonucleoprotein K
KeywordsSIGNALING PROTEIN / Brd4 / hnRNPK / acetyllysine
Function / homology
Function and homology information


regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / podosome / negative regulation of mRNA splicing, via spliceosome / RNA polymerase II C-terminal domain binding / P-TEFb complex binding ...regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of low-density lipoprotein particle clearance / random inactivation of X chromosome / regulatory ncRNA-mediated heterochromatin formation / regulation of mRNA splicing, via spliceosome / SUMOylation of RNA binding proteins / podosome / negative regulation of mRNA splicing, via spliceosome / RNA polymerase II C-terminal domain binding / P-TEFb complex binding / Processing of Capped Intron-Containing Pre-mRNA / 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 / RNA processing / : / catalytic step 2 spliceosome / RNA polymerase II CTD heptapeptide repeat kinase activity / mRNA Splicing - Major Pathway / HCMV Late Events / condensed nuclear chromosome / transcription coregulator activity / cell projection / positive regulation of transcription elongation by RNA polymerase II / mRNA splicing, via spliceosome / cytoplasmic stress granule / 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 / cadherin binding / chromatin remodeling / ribonucleoprotein complex / protein domain specific binding / focal adhesion / negative regulation of DNA-templated transcription / protein serine/threonine kinase activity / mRNA binding / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
ROK, N-terminal / ROKNT (NUC014) domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / Brdt, bromodomain, repeat I / Brdt, bromodomain, repeat II ...ROK, N-terminal / ROKNT (NUC014) domain / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / 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 / K Homology domain / K homology RNA-binding domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily
Similarity search - Domain/homology
ACETATE ION / Bromodomain-containing protein 4 / Heterogeneous nuclear ribonucleoprotein K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.1Oct 16, 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

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4
B: Heterogeneous nuclear ribonucleoprotein K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5237
Polymers16,1982
Non-polymers3255
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-29 kcal/mol
Surface area7870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.454, 52.080, 53.325
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 15099.380 Da / Num. of mol.: 1 / Fragment: UNP residues 44-168
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRD4, HUNK1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: O60885
#2: Protein/peptide Heterogeneous nuclear ribonucleoprotein K / hnRNP K / Transformation up-regulated nuclear protein / TUNP


Mass: 1098.317 Da / Num. of mol.: 1 / Fragment: UNP residues 57-66 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P61978

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Non-polymers , 4 types, 158 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.08 Å3/Da / Density % sol: 40.78 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% w/v PEG3350, 0.2 M ammonium acetate, 0.1 M Bis-Tris

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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: Sep 16, 2019
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: 1.38→24.23 Å / Num. obs: 27852 / % possible obs: 98.9 % / Redundancy: 9.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.018 / Rrim(I) all: 0.057 / Net I/σ(I): 22.3 / Num. measured all: 263623 / 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
1.38-1.417.10.683909912750.9070.2630.7362.492.4
7.58-24.237.60.05315812070.9960.020.05644.896.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.54 Å24.23 Å
Translation4.54 Å24.23 Å

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Processing

Software
NameVersionClassificationNB
PHENIXdev_3940refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3MXF

3mxf


Resolution: 1.38→24.23 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1979 1404 5.05 %
Rwork0.1761 26397 -
obs0.1771 27801 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 67.69 Å2 / Biso mean: 25.7296 Å2 / Biso min: 11.14 Å2
Refinement stepCycle: final / Resolution: 1.38→24.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1116 0 43 154 1313
Biso mean--42.51 30.26 -
Num. residues----135
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.38-1.430.31911250.32512485261094
1.43-1.490.31591390.30082578271798
1.49-1.560.24081450.23682590273599
1.56-1.640.24111400.19492587272799
1.64-1.740.21611500.20652641279199
1.74-1.880.20721210.18552651277299
1.88-2.070.19452030.157925992802100
2.07-2.370.17371220.154926922814100
2.37-2.980.18231140.156727462860100
2.98-24.230.18461450.169428282973100
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)
14.7198-4.035-4.14623.88062.43366.52650.0073-0.3599-0.07760.27520.18640.2940.2805-0.5104-0.17690.22850.0297-0.01590.38940.01030.2262-21.263512.8477-19.0952
23.4994-0.224-4.6953.08511.40156.6946-0.04161.17380.0416-0.39820.03040.0654-0.1775-0.1359-0.09440.2490.0152-0.01960.4343-0.03530.1757-4.50235.4924-31.5081
34.2819-1.9329-2.92441.8921.36152.7741-0.026-0.0028-0.18070.1005-0.01450.05970.18630.02770.04860.1383-0.0184-0.00730.1183-0.00990.1523-3.31542.1231-12.2966
45.2145-2.3598-0.88523.14131.34993.3716-0.1748-0.21960.0320.0896-0.05280.2889-0.2596-0.50950.17150.13190.0344-0.03450.2145-0.02930.1226-14.928611.7834-15.0922
53.6116-1.0261-1.05672.05011.31325.61090.02760.25190.069-0.2380.1158-0.1957-0.22010.4459-0.10560.1422-0.01480.02990.18620.00130.13850.99449.2535-24.0624
62.2005-1.3022-0.7942.9791.72973.16980.0288-0.109-0.01830.01240.0284-0.0630.00430.1134-0.05190.0966-0.0298-0.00080.1064-0.00030.1073-2.654912.4439-7.5831
73.6038-0.7545-1.85272.1457-1.76614.7045-0.1653-0.1541-0.30340.1792-0.02490.09470.1643-0.24950.17530.1793-0.0390.02620.1887-0.03380.1984-16.521312.47360.1898
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 42:48)A42 - 48
2X-RAY DIFFRACTION2(chain A and resid 49:58)A49 - 58
3X-RAY DIFFRACTION3(chain A and resid 59:87)A59 - 87
4X-RAY DIFFRACTION4(chain A and resid 88:116)A88 - 116
5X-RAY DIFFRACTION5(chain A and resid 117:126)A117 - 126
6X-RAY DIFFRACTION6(chain A and resid 127:166)A127 - 166
7X-RAY DIFFRACTION7(chain B and resid 57:66)B57 - 66

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