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- PDB-6uls: BRD4-BD1 in complex with the a diacetylated-E2F1 peptide -

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Basic information

Entry
Database: PDB / ID: 6uls
TitleBRD4-BD1 in complex with the a diacetylated-E2F1 peptide
Components
  • Bromodomain-containing protein 4
  • Diacetylated E2F1 Peptide (K117ac and K120ac)
KeywordsTRANSCRIPTION / BET / bromodomain / E2F1 / BRD4 / acetylated
Function / homology
Function and homology information


Rb-E2F complex / lens fiber cell apoptotic process / negative regulation of fat cell proliferation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / mRNA stabilization / anoikis / Activation of NOXA and translocation to mitochondria / Activation of PUMA and translocation to mitochondria ...Rb-E2F complex / lens fiber cell apoptotic process / negative regulation of fat cell proliferation / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / Transcription of E2F targets under negative control by DREAM complex / mRNA stabilization / anoikis / Activation of NOXA and translocation to mitochondria / Activation of PUMA and translocation to mitochondria / DNA-binding transcription activator activity / G1/S-Specific Transcription / negative regulation of fat cell differentiation / G2 Phase / Transcriptional Regulation by E2F6 / negative regulation of DNA binding / regulation of G1/S transition of mitotic cell cycle / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / intrinsic apoptotic signaling pathway by p53 class mediator / P-TEFb complex binding / negative regulation by host of viral transcription / cis-regulatory region sequence-specific DNA binding / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / positive regulation of T-helper 17 cell lineage commitment / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / forebrain development / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / DNA damage checkpoint signaling / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / lysine-acetylated histone binding / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / Cyclin D associated events in G1 / intrinsic apoptotic signaling pathway in response to DNA damage / sequence-specific double-stranded DNA binding / positive regulation of fibroblast proliferation / p53 binding / cellular response to xenobiotic stimulus / chromosome / regulation of inflammatory response / Oxidative Stress Induced Senescence / DNA-binding transcription factor binding / positive regulation of canonical NF-kappaB signal transduction / sequence-specific DNA binding / Potential therapeutics for SARS / molecular adaptor activity / transcription coactivator activity / protein dimerization activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / centrosome / DNA damage response / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / Bromodomain protein 4, C-terminal / C-terminal domain of bromodomain protein 4 / NET domain superfamily ...E2F transcription factor, CC-MB domain / E2F transcription factor CC-MB domain / E2F Family / E2F-DP heterodimerization region / E2F/DP family, winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / E2F/DP family winged-helix DNA-binding domain / 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 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Bromodomain-containing protein 4 / Transcription factor E2F1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsPatel, K. / Low, J.K.K. / Mackay, J.P.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1161623 Australia
CitationJournal: Biochemistry / Year: 2021
Title: BET-Family Bromodomains Can Recognize Diacetylated Sequences from Transcription Factors Using a Conserved Mechanism.
Authors: Patel, K. / Solomon, P.D. / Walshe, J.L. / Ford, D.J. / Wilkinson-White, L. / Payne, R.J. / Low, J.K.K. / Mackay, J.P.
History
DepositionOct 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 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: Diacetylated E2F1 Peptide (K117ac and K120ac)


Theoretical massNumber of molelcules
Total (without water)18,2472
Polymers18,2472
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area7700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.309, 50.350, 54.246
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 17200.648 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 Diacetylated E2F1 Peptide (K117ac and K120ac)


Mass: 1046.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01094*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.81 Å3/Da / Density % sol: 31.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M MMT pH 7.0, 25% w/v PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.5→48.31 Å / Num. obs: 21857 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 11.49 Å2 / CC1/2: 0.999 / Net I/σ(I): 32.5
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1070 / CC1/2: 0.982

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LYI

4lyi


Resolution: 1.5→36.9 Å / SU ML: 0.1484 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.258
RfactorNum. reflection% reflection
Rfree0.2043 1210 5.55 %
Rwork0.1702 --
obs0.172 21804 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.27 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 1 155 1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841152
X-RAY DIFFRACTIONf_angle_d0.97711566
X-RAY DIFFRACTIONf_chiral_restr0.0529165
X-RAY DIFFRACTIONf_plane_restr0.0061204
X-RAY DIFFRACTIONf_dihedral_angle_d12.1428705
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.560.25411400.21332233X-RAY DIFFRACTION99.87
1.56-1.630.21071330.1862259X-RAY DIFFRACTION99.92
1.63-1.720.19521450.16422223X-RAY DIFFRACTION100
1.72-1.820.18281620.1642234X-RAY DIFFRACTION100
1.82-1.970.20471110.15612291X-RAY DIFFRACTION100
1.97-2.160.1991290.1572288X-RAY DIFFRACTION100
2.16-2.480.22381050.16612321X-RAY DIFFRACTION100
2.48-3.120.18961440.17482305X-RAY DIFFRACTION100
3.12-36.90.20941410.17282440X-RAY DIFFRACTION99.92
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)
14.38801381525-5.792606047474.840290449357.80185722233-6.029224212316.63901332250.2050224638420.460057805764-0.0691947930954-0.382751568037-0.157509370590.01762084504630.4156131829740.36555661838-0.1273976682860.1821577947540.04428194281970.02379894985580.222602589725-0.02074517187470.12442468436515.4581928302-9.27507522468-23.8139453012
24.71410281852-4.52666751761-0.8118188852927.007400249563.122101387093.51080120612-0.0961253680721.010621476240.0578164566492-0.423273444875-0.0900875587017-0.106495334955-0.277807989994-0.1215457748580.1624177836380.247890069228-0.0413130536535-0.004436150650920.3020886982520.01632999575030.123444520575-0.928043374126-2.9218655581-32.1691615353
34.3737898276-1.644754209851.072565497062.450070712770.03086746745656.30709656093-0.03584027838610.0619102094835-0.1179554087250.05561246678940.0984517237440.222544577452-0.0951499324805-0.118750854886-0.1174939961190.09018617823220.006415209978820.01391742488090.0527579853290.024234623430.0824675725764-5.09214514509-0.00473653600923-19.3133878053
44.39924824771-0.5166255449672.645254142680.986967926008-0.8277046712842.36466865369-0.104560031192-0.1449564772080.4388969613420.0262013628999-0.0134807130502-0.0749790600167-0.356477828123-0.130616921590.1143404845940.1177941087420.0123558634381-0.003150467465020.0648802127201-0.0209131341150.1258779425523.49294812278-0.35018033443-7.91862370083
51.76384672599-0.989234224083-0.7356330238453.794243449020.7493595656085.933528955220.117485387325-0.1777021517160.25378750078-0.04910647949220.176145460245-0.290155471767-0.1948870715630.237402396632-0.2639978201170.08134860355-0.0110885738128-0.01096469725680.0832500700651-0.0199333609210.12455449608114.6413104111-5.73054757418-9.85682349904
68.132836754950.6163175911121.627430211040.757851926585-1.035837318292.38042560453-0.276737414121-0.7407926283330.5830350259720.2052288934690.0512810033423-0.516873635405-0.160892329327-0.0278898932690.1523582828540.1283813124730.0905322111314-0.06381217367470.352361970414-0.1271849666440.26058317745324.2874668182-13.6187475239-9.20109064637
73.31480762217-1.645572996481.900248552832.09161184557-2.063630027422.924690431310.03780645390860.114848294737-0.0154528513471-0.119746997925-0.04514626722060.02905212331040.1319636102740.06377351442290.00771899116420.0916618914088-0.008519246428310.0157315344160.0806869583896-0.01508545051430.06486011481138.41476344614-9.22460166767-20.1654813771
83.56658337751-2.391520429042.261713744112.62305479799-2.792800525384.965866543760.04560260909110.0107160693115-0.111793939416-0.1855422210970.1285110657740.1329496467010.152912632755-0.163794385289-0.1913850501480.104409188002-0.02958196386450.002568125224180.06897019923490.001961204515820.08979147930713.894998416-13.7966839255-14.4532664782
93.913862570182.98142916145-4.070339169457.902754132731.505306627518.01244268710.014951259989-0.145423344725-0.3003611020630.371019700921-0.109768509536-0.1784916811150.4730098832220.1253430582530.07577694625350.109719912338-0.000704614760618-0.01360238525070.0932988237240.02547949152430.094463416463912.1096631663-18.2596811270.199315698106
106.70687940527-1.766185182843.44631127882.74301840927-1.804090675394.727819792760.04026299963550.0329766194012-0.01515715609140.02680754499640.1028274311290.226932938718-0.0642741571836-0.148390585982-0.1730265549730.0909352624505-0.01654599133640.02604243063790.057366460302-0.003294996792080.0840467312995-1.54147793047-8.39867267442-6.61728135689
112.78411937297-1.03795831479-0.2399016711033.277384984910.9787708229253.15839549675-0.0113221423181-0.127408915751-0.01074499498240.08108668908020.123506420098-0.2369348834270.09515128689170.0453340660758-0.1500789189840.08433587848590.00390484762686-0.01246527551110.09569841938640.002494485694760.11458534172216.2284607913-9.01070303808-0.552121694162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 52 )
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 60 )
3X-RAY DIFFRACTION3chain 'A' and (resid 61 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 80 )
5X-RAY DIFFRACTION5chain 'A' and (resid 81 through 88 )
6X-RAY DIFFRACTION6chain 'A' and (resid 89 through 96 )
7X-RAY DIFFRACTION7chain 'A' and (resid 97 through 121 )
8X-RAY DIFFRACTION8chain 'A' and (resid 122 through 139 )
9X-RAY DIFFRACTION9chain 'A' and (resid 140 through 144 )
10X-RAY DIFFRACTION10chain 'A' and (resid 145 through 166 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 11 )

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