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- PDB-9kt2: The crystal structure of BD1 in complex with BDS4 -

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Basic information

Entry
Database: PDB / ID: 9kt2
TitleThe crystal structure of BD1 in complex with BDS4
ComponentsBromodomain-containing protein 4
KeywordsUNKNOWN FUNCTION / BD1 / BDS4 / compiex
Function / homology
Function and homology information


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 / : / RNA polymerase II CTD heptapeptide repeat kinase activity / condensed nuclear chromosome ...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 / : / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46206515118 Å
AuthorsZhang, Z.M. / Wang, Y.Q.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Inhibition of BD1 of the BET proteins through covalent modification of lysine in living cells and animals
Authors: Zhang, Z.M. / Wang, Y.Q.
History
DepositionDec 1, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 3, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain-containing protein 4


Theoretical massNumber of molelcules
Total (without water)15,4861
Polymers15,4861
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.114, 55.444, 57.53
Angle α, β, γ (deg.)90.0, 90.0, 90.0
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: 15485.846 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.88 Å3/Da / Density % sol: 34.5 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / Details: 0.15 M potassium bromide, 30% (v/v) PEG2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CAMD / Beamline: GCPCC / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Nov 25, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.461→29.98 Å / Num. obs: 20044 / % possible obs: 99.69 % / Redundancy: 9.8 % / Biso Wilson estimate: 21.92 Å2 / CC1/2: 0.998 / Net I/σ(I): 15
Reflection shellResolution: 1.461→1.513 Å / Num. unique obs: 20044 / CC1/2: 0.998

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Processing

Software
NameVersionClassification
PHENIX1.9_1692+SVNrefinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.46206515118→29.9721530856 Å / SU ML: 0.118822104985 / Cross valid method: FREE R-VALUE / σ(F): 1.33554249965 / Phase error: 18.9106965038
RfactorNum. reflection% reflection
Rfree0.194724778156 2002 10.0140056022 %
Rwork0.166075405785 17990 -
obs0.169022743704 19992 99.710723192 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.9232303211 Å2
Refinement stepCycle: LAST / Resolution: 1.46206515118→29.9721530856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 34 145 1227
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006844905879141118
X-RAY DIFFRACTIONf_angle_d1.392152474461527
X-RAY DIFFRACTIONf_chiral_restr0.0732517522019158
X-RAY DIFFRACTIONf_plane_restr0.00519542980035193
X-RAY DIFFRACTIONf_dihedral_angle_d17.4427069699419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4621-1.49860.2458362914491380.2239703261861236X-RAY DIFFRACTION98.2832618026
1.4986-1.53910.2415619503331460.1973785007891269X-RAY DIFFRACTION99.718111346
1.5391-1.58440.2215198297391370.1809782197441254X-RAY DIFFRACTION100
1.5844-1.63560.19790586091350.1733287816121285X-RAY DIFFRACTION100
1.6356-1.6940.2240034063811460.1815121860171263X-RAY DIFFRACTION100
1.694-1.76180.2035573044141380.1907384028011266X-RAY DIFFRACTION100
1.7618-1.8420.2146706762531470.1782527735981272X-RAY DIFFRACTION99.8592540464
1.842-1.93910.2097497451131420.1710109641011289X-RAY DIFFRACTION99.9301675978
1.9391-2.06060.2294727517891400.1796742420231267X-RAY DIFFRACTION99.4346289753
2.0606-2.21960.2233274745181430.1701610003591280X-RAY DIFFRACTION99.5801259622
2.2196-2.44290.1793853759291430.1619784671551285X-RAY DIFFRACTION99.5815899582
2.4429-2.79620.2110518000861440.1662876807031303X-RAY DIFFRACTION100
2.7962-3.5220.1680659247461480.1603164258881328X-RAY DIFFRACTION99.932295193
3.522-29.970.1732850697921550.1481806326211393X-RAY DIFFRACTION99.6138996139
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)
10.858976164843-0.121812398831-0.134328072120.953691872659-0.08891038407582.229215145950.02562035332410.005884181792190.1142584459560.005902163283870.00600609930707-0.0699408515489-0.08115561019810.103069847512-0.01375683477670.134720139702-0.00821872357868-0.002233399875680.118377984607-9.85534260831E-50.146275772141-0.977758220993-2.059858085952.78265898447
21.57776432696-0.3328076049690.03039645413942.34843350364-0.3633275710662.62560059386-0.0569590198952-0.4031985351870.083541530090.3167438135340.030306074023-0.08230214753040.08009535819410.01911246358980.007224141807470.1976505718330.000537639820987-0.01013099360860.227134127989-0.04154115251520.168526840047-0.0829183959499-7.9995300689921.8714432934
30.9536739018530.151636893886-0.3966406299911.155384827950.1614441123111.91231357310.022270729447-0.0714122442420.02033470763710.03123596907690.0194228780902-0.0769453277243-0.03688723106280.0928805139033-0.02409115868560.1218112317280.00578139925595-0.007731009761760.135184346658-0.01115972927190.1355304340270.836393198418-9.541533391066.30998694857
42.503431961190.133124403717-0.1207825642271.60247696987-0.3421712709853.84893289869-0.0371464176782-0.00661132459932-0.0660418944790.06716389923710.04677850129510.215177345618-0.0486940607852-0.478542347019-0.08180392876870.122098779737-0.01937369834110.001999593851860.1365141834830.004145766671460.181125830321-13.2587126605-10.97358474657.83809739771
58.40631496459-0.341308772673-0.8562417460424.49620540057-0.1215415160645.70008890590.05751719720070.3997005752750.287468277365-0.490493334039-0.255367824744-0.1509038278880.334857445264-0.05953689238440.1956592422730.1953554599770.0259603025699-0.02775422448120.2431037253970.02216910236490.144927293154-4.26873801265-6.45080297081-13.6850225028
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 43 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 139 )
4X-RAY DIFFRACTION4chain 'A' and (resid 140 through 163 )
5X-RAY DIFFRACTION5chain 'A' and (resid 164 through 168 )

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