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- PDB-8b5b: Human BRD4 bromdomain 1 in complex with a H4 peptide containing a... -

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Basic information

Entry
Database: PDB / ID: 8b5b
TitleHuman BRD4 bromdomain 1 in complex with a H4 peptide containing acetyl lysine and ApmTri (H4K5acK8ApmTri)
Components
  • Bromodomain-containing protein 4BRD4
  • H4K5acK8ApmTri
KeywordsPEPTIDE BINDING PROTEIN / ApmTri / acetyl-lysine mimic / BET-Bromodomain / histone-peptide
Function / homology
Function and homology information


RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity ...RNA polymerase II C-terminal domain binding / negative regulation of DNA damage checkpoint / P-TEFb complex binding / negative regulation by host of viral transcription / positive regulation of T-helper 17 cell lineage commitment / positive regulation of G2/M transition of mitotic cell cycle / histone reader activity / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome / transcription coregulator activity / positive regulation of transcription elongation by RNA polymerase II / lysine-acetylated histone binding / p53 binding / chromosome / regulation of inflammatory response / positive regulation of canonical NF-kappaB signal transduction / Potential therapeutics for SARS / transcription coactivator activity / transcription cis-regulatory region binding / chromatin remodeling / DNA damage response / chromatin binding / regulation of transcription by RNA polymerase II / 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 / 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 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
DI(HYDROXYETHYL)ETHER / Bromodomain-containing protein 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsBraun, M.B. / Bartlick, N. / Stehle, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SCHW 1163/9-1 Germany
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Synthesis, Biochemical Characterization, and Genetic Encoding of a 1,2,4-Triazole Amino Acid as an Acetyllysine Mimic for Bromodomains of the BET Family.
Authors: Kirchgassner, S. / Braun, M.B. / Bartlick, N. / Koc, C. / Reinkemeier, C.D. / Lemke, E.A. / Stehle, T. / Schwarzer, D.
History
DepositionSep 22, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.0May 24, 2023Group: Non-polymer description / Category: chem_comp / Item: _chem_comp.formula
Revision 2.1Feb 7, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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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: Bromodomain-containing protein 4
D: H4K5acK8ApmTri
E: H4K5acK8ApmTri
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4656
Polymers48,3595
Non-polymers1061
Water4,486249
1
A: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)15,2951
Polymers15,2951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-0 kcal/mol
Surface area7550 Å2
MethodPISA
2
B: Bromodomain-containing protein 4
D: H4K5acK8ApmTri


Theoretical massNumber of molelcules
Total (without water)16,5322
Polymers16,5322
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-7 kcal/mol
Surface area7320 Å2
MethodPISA
3
C: Bromodomain-containing protein 4
E: H4K5acK8ApmTri
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6383
Polymers16,5322
Non-polymers1061
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-9 kcal/mol
Surface area7540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.508, 51.780, 170.739
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 / BRD4 / Protein HUNK1


Mass: 15294.578 Da / Num. of mol.: 3
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 H4K5acK8ApmTri


Mass: 1237.416 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: acetylated lysine and non-natural amino acid ApmTri containing H4 peptide
Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM sodium acetate trihydrate 100 mM Trishydrochloride pH 8.5 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000029 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000029 Å / Relative weight: 1
ReflectionResolution: 1.92→44.3 Å / Num. obs: 27441 / % possible obs: 99.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 24.7 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.85
Reflection shellResolution: 1.92→2.04 Å / Num. unique obs: 4283 / CC1/2: 0.62

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OSS

2oss


Resolution: 1.92→44.27 Å / SU ML: 0.2397 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1926
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2462 1098 4 %
Rwork0.1969 26338 -
obs0.1989 27436 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.91 Å2
Refinement stepCycle: LAST / Resolution: 1.92→44.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 7 249 3448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313303
X-RAY DIFFRACTIONf_angle_d0.57214504
X-RAY DIFFRACTIONf_chiral_restr0.0373482
X-RAY DIFFRACTIONf_plane_restr0.0034584
X-RAY DIFFRACTIONf_dihedral_angle_d6.11842242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-2.010.31111320.28543163X-RAY DIFFRACTION97.63
2.01-2.110.34391340.26023215X-RAY DIFFRACTION98.76
2.11-2.240.24141360.23413258X-RAY DIFFRACTION98.95
2.24-2.420.28741350.22783244X-RAY DIFFRACTION99.09
2.42-2.660.28091350.21453259X-RAY DIFFRACTION99.09
2.66-3.050.27671400.20483338X-RAY DIFFRACTION99.57
3.05-3.840.22641390.17273341X-RAY DIFFRACTION99.86
3.84-44.270.19451470.15773520X-RAY DIFFRACTION99.51
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)
17.81257927234-4.33442172843-4.173200368776.220370359164.077641336029.44760712794-0.009283500179380.666132034633-0.8104207882540.180238687181-0.214460701370.228074647934-0.308627761992-0.5079850376940.2534125671650.207120419593-0.0181112086122-0.03537365608890.261045703519-0.02971806252120.278832787962-19.412442792215.9730703623-19.7133778594
24.60787184993-1.6362996061-2.610069580497.01001611643-3.076427684369.095967785390.1278831075870.0970921781593-0.0607000787917-0.2800597815580.215926714986-0.2976897713520.5849712855460.218310219536-0.3546862790070.242260246164-0.0293693950099-0.04136563960430.189438542182-0.04954909062090.3371375864421.790698788118.94379915965-29.4758241613
37.14067886664-2.335279594151.511690515622.99201969492-1.143236835172.109472158810.0452262126229-0.232408512431-0.3180039666210.1025640801210.0461769958470.06013159619260.0406065196993-0.0315206014648-0.06560840081530.229632400786-0.0370313326156-0.01625781329230.15556188829-0.02188070626170.179879535395-10.942469366612.1451990051-11.0598196575
48.14903513643.84557029816-6.017194171074.30377731818-3.331971145144.57974569135-0.4951563489120.527750837286-0.412365826703-0.2726975086130.1493774274050.0797651720850.5977889708-0.3556918005170.391207463170.225063270973-0.01161694481490.001134494233860.196384824971-0.02907427856880.208138137181-4.4827914361410.2535911207-25.0875216649
55.57950537089-0.280049111214-3.715957810361.436912585581.474936117249.764218918010.0658908372434-0.06706594416490.0547120875836-0.07830275839-0.1539667520360.056840745244-0.3452385950510.1292772554950.06771488858640.1993924935270.0172400547699-0.04216732442050.183229015412-0.0251926875040.272347664353-3.8272159797918.303119084-13.3820167279
67.21913113401-1.06073158664-2.967786915933.253571990482.383507845019.37692930924-0.0824135776697-0.336024155877-0.2188379638520.08262808648110.132495299523-0.2604682651790.3466618258740.675804700824-0.02108194528670.1992990524840.0124559027271-0.04895099252620.1598651410450.01296142322410.2747861690892.8054889081112.5722835697-8.98395508784
76.96619071756-0.620732646566-2.525892117783.20084193419-3.177588292644.593421153810.2622298022220.415173759487-0.242695136269-0.6125810279020.157987441170.542914336170.541343371137-1.0494223744-0.406610062320.230461713886-0.0136159001161-0.05798624175480.3418090539940.06179711403270.288396840635-42.069190507319.6504658204-38.3895323862
85.18520892662-1.427554196455.255809974822.86698070793-1.466701145355.301544975350.0282308562374-0.705762741824-0.7816387232660.4043033549460.2354952160620.2421867812760.184246465128-1.15366494912-0.3573558662770.2688344272250.011893790084-0.003139074239440.4422375675550.001806437358910.299257757868-30.02985140823.5171461768-23.1065784575
93.262554328620.754059740318-5.161517243132.146947756690.1340630208669.23868572760.002793419158920.1516442555220.464037889173-0.325857610348-0.3187662321730.359609925118-0.3795382440140.4588480822690.3543901815260.2985952854030.0639507217297-0.003888566767940.3585057945260.03880169799220.347346615126-17.430011653527.1817245085-21.5365323056
107.677449275595.043611120320.8927553888068.63594423392-1.768330251187.25462566058-0.2207859006470.06090411459990.663376201658-0.116278157026-0.292201201711-0.067419568852-0.4383685402840.6598971420660.4510776740810.2103702853410.01264109267680.04688069010190.235704471283-0.004267743768930.33566859358-16.149897530931.3354108172-35.0717585493
113.242997947450.08886404709360.8451625161982.609255905141.416866398174.760769664790.04793774350350.3293077117930.480648568167-0.167308760035-0.08639060801580.02706892603560.0349996543728-0.156368857730.03896839308770.1882308085030.03032878549820.02895155683290.2534744880380.04857781787230.237367492855-30.259665070624.2139638689-40.1404954154
122.008958844640.7888237307151.490510959170.8626523585741.767165407318.772725445590.1722580499650.6471066830470.0817142313686-0.136611994575-0.0878756317245-0.1120586148540.4525520579170.70891984361-0.1501913781560.2524149432250.09252507450320.0418111433070.34693580518-0.0005433240218610.208747086243-23.148910115519.5302247628-43.193837154
135.969719174831.177150197221.421981024773.002607790841.948157207585.291906806240.2560010430570.971879297422-0.389607989994-0.07333232735620.485883058246-0.3544482671160.05101355071671.08546080966-0.5283397365830.1762788609650.04693522193290.0481882173220.4999976526280.03115122098770.290246538885-11.966610422525.5524379762-41.8549734649
146.163610120856.50881802126-6.50188455157.47163266114-6.076497209348.176109578270.214432085063-0.813127355075-0.3753820646870.0234058909592-0.443491549385-0.428579038803-0.1133196602980.6524763615290.2685936683050.1979768612760.017700679097-0.01633005970720.2936201347390.0155759246530.261840484708-16.582581348239.8312784357-8.16307540813
154.14847263551-0.2164616883594.770575209795.24931374214-2.194699242436.231856157490.1695653405020.57525555058-0.573046750939-0.1593357054960.0192964015657-0.2376182749140.1470089557340.0950753738303-0.2227521644650.1842046435180.02104945045570.02688755323140.275889296055-0.05104303011120.197864620066-33.620987662929.30104184453.96466391351
166.162214328275.350780466642.995289010346.433774752172.784302483567.63943093293-0.137011482978-0.4345805467820.571096059196-0.1047032375610.1137872726440.1446553227340.304764808107-1.046105982920.01332166665420.208635623883-0.00762382677211-0.0599818509640.158868783872-0.02086065422930.24661460523-41.379820218628.0919484487-8.35430869964
175.516941764942.437794958370.9680070366562.466420524650.08261647026741.55333632741-0.03760939683030.520193482708-0.168670038763-0.1938948826350.155409867796-0.1099849080790.05953525667420.159192594519-0.1204856060640.1741085683820.0503124242039-0.007409531154960.188395789758-0.0184772885710.167986009743-25.44264451339.6573104792-17.5072768879
185.974621007790.821864506198-4.961225570641.90568596574-0.858757505624.174735762820.0711677767879-0.0316736713224-0.201251713359-0.1794457704070.0864651370513-0.1518856441330.4208548901120.1521748148-0.1775697059890.1889249867210.0417857401091-0.03130665660180.21184490807-0.0267273998790.189995851335-31.887713838731.9897811262-4.82445474221
197.450841626075.55846930821-6.521715725456.82601121942-5.880878002276.478016252060.261250398440.4144347496840.2471582893970.1228276654520.06027980761080.223144933303-0.291638570102-0.300565185011-0.3961343158840.1576677490610.0570665010554-0.0278491214130.194945469977-0.03046405431940.203515384588-32.153174658844.895923171-14.3170733878
208.214775444222.43866053456-2.235398043947.497025534450.3043690304224.99991187576-0.1887023170341.04411236615-0.489459679825-0.9249232595590.09100248961230.0601623043959-0.500610898822-0.3194772009840.09633313964850.2972472456380.0429011685113-0.02584099123440.31221000718-0.07906561703420.192853317937-30.639083177644.1720652741-26.0782944876
214.700569910380.235828516664-4.053632804395.3110552999-0.950285925466.75927852144-0.1086308752990.00847118451218-0.646723064892-0.002026780641810.07808814748720.2052841973280.0110742879433-0.0965712828144-0.08269856379720.2184753856280.0642524895235-0.09428218048360.3279754451090.01004570874430.319036848645-43.548910472337.9169926104-16.474739427
226.04728867512-1.2949301137-2.969562703465.727543257540.9797956502857.86079810568-0.2265262412210.9419821182070.381282298462-0.155047679994-0.5203817381860.4948909472720.4484787955520.8798682965030.2889987397020.2959174683890.0311267971333-0.0230930839990.5188712187370.1488326564540.296698612873-33.17892729522.8430906748-53.7517514952
238.319665698954.353930756984.031825020484.352825768660.9715346348042.54795058351-0.07118401084240.4859591310010.426348199576-0.1748064723360.0980772343992-0.0255463737968-0.591403866465-0.0227417378301-0.01260409935160.3007610083140.06024654943240.0007618130151280.2839502614520.03649783287170.283010452473-22.661233272446.0445522144-25.5454396309
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 68 )
3X-RAY DIFFRACTION3chain 'A' and (resid 69 through 105 )
4X-RAY DIFFRACTION4chain 'A' and (resid 106 through 121 )
5X-RAY DIFFRACTION5chain 'A' and (resid 122 through 141 )
6X-RAY DIFFRACTION6chain 'A' and (resid 142 through 167 )
7X-RAY DIFFRACTION7chain 'B' and (resid 42 through 47 )
8X-RAY DIFFRACTION8chain 'B' and (resid 48 through 55)
9X-RAY DIFFRACTION9chain 'B' and (resid 56 through 60 )
10X-RAY DIFFRACTION10chain 'B' and (resid 61 through 75 )
11X-RAY DIFFRACTION11chain 'B' and (resid 76 through 119 )
12X-RAY DIFFRACTION12chain 'B' and (resid 120 through 150 )
13X-RAY DIFFRACTION13chain 'B' and (resid 151 through 166 )
14X-RAY DIFFRACTION14chain 'C' and (resid 40 through 51)
15X-RAY DIFFRACTION15chain 'C' and (resid 52 through 60 )
16X-RAY DIFFRACTION16chain 'C' and (resid 61 through 68 )
17X-RAY DIFFRACTION17chain 'C' and (resid 69 through 106 )
18X-RAY DIFFRACTION18chain 'C' and (resid 107 through 121 )
19X-RAY DIFFRACTION19chain 'C' and (resid 122 through 144 )
20X-RAY DIFFRACTION20chain 'C' and (resid 145 through 150 )
21X-RAY DIFFRACTION21chain 'C' and (resid 151 through 166 )
22X-RAY DIFFRACTION22chain 'D' and (resid 2 through 9 )
23X-RAY DIFFRACTION23chain 'E' and (resid 0 through 10 )

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