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- PDB-5vbr: CRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRDT IN COMPL... -

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Basic information

Entry
Database: PDB / ID: 5vbr
TitleCRYSTAL STRUCTURE OF THE FIRST BROMODOMAIN OF HUMAN BRDT IN COMPLEX WITH Volasertib
ComponentsBromodomain testis-specific protein
KeywordsTRANSCRIPTION/INHIBITOR / BROMODOMAIN / CAP / HUNK1 / MCAP / PROTEIN BINDING-INHIBITOR COMPLEX / MITOTIC CHROMOSOME ASSOCIATED PROTEIN / INHIBITOR / TRANSCRIPTION-INHIBITOR COMPLEX
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / regulation of DNA-templated transcription / positive regulation of gene expression / 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
Chem-IBI / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsEMBER, S.W. / ZHU, J.-Y. / SCHONBRUNN, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)HD076542-01S1 United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors.
Authors: Karim, R.M. / Bikowitz, M.J. / Chan, A. / Zhu, J.Y. / Grassie, D. / Becker, A. / Berndt, N. / Gunawan, S. / Lawrence, N.J. / Schonbrunn, E.
History
DepositionMar 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.3Nov 17, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bromodomain testis-specific protein
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,63017
Polymers26,6392
Non-polymers1,99115
Water4,035224
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3469
Polymers13,3191
Non-polymers1,0278
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2848
Polymers13,3191
Non-polymers9657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint5 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.450, 31.050, 69.800
Angle α, β, γ (deg.)90.000, 97.090, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Bromodomain testis-specific protein / Cancer/testis antigen 9 / CT9 / RING3-like protein


Mass: 13319.365 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 29-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) STAR / References: UniProt: Q58F21
#2: Chemical ChemComp-IBI / N-{trans-4-[4-(cyclopropylmethyl)piperazin-1-yl]cyclohexyl}-4-{[(7R)-7-ethyl-5-methyl-8-(1-methylethyl)-6-oxo-5,6,7,8-tetrahydropteridin-2-yl]amino}-3-methoxybenzamide / Volasertib / Volasertib


Mass: 618.813 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H50N8O3 / Comment: anticancer, inhibitor*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 8 MG/ML BRDT, 25MM HEPES PH 7.5, 75MM SODIUM CHLORIDE, 0.5MM DTT, 50MM MES PH 6.5, 0.1M AMMONIUM, SULFATE, 15% PEG MME 5,000, 10% DMSO, 1 MM Volasertib

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2014
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→69.267 Å / Num. obs: 22421 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 13.91 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.092 / Χ2: 0.984 / Net I/σ(I): 15.45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.953.7190.4173.6816520.8680.48999.9
1.95-23.7070.3334.6315780.8990.39199.7
2-2.063.7250.2685.5815770.9380.31499.7
2.06-2.123.7030.2176.9514970.9510.25599.9
2.12-2.193.7120.1778.2414730.9720.20899.9
2.19-2.273.7130.1688.5714070.9740.19799.6
2.27-2.363.7350.1410.1113650.9810.16499.8
2.36-2.453.7320.13510.6313120.9820.15899.5
2.45-2.563.7280.10512.8112790.990.12399.8
2.56-2.693.720.08814.8112060.9920.10399.8
2.69-2.833.7260.07716.8511840.9920.09199.9
2.83-33.7170.06219.8510830.9950.073100
3-3.213.7270.05223.1410360.9960.06199.4
3.21-3.473.7170.04227.679790.9980.04999.7
3.47-3.83.6810.03532.988850.9980.041100
3.8-4.253.6650.0335.778110.9990.03599.6
4.25-4.913.6550.02539.427040.9990.0399
4.91-6.013.6140.02734.446290.9990.03299.8
6.01-8.53.5220.02735.034810.9990.03299.6
8.5-69.2673.1910.02338.032830.9990.02897.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
SERGUIdata collection
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCX

4kcx


Resolution: 1.9→69.267 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.97
RfactorNum. reflection% reflection
Rfree0.2012 1120 5 %
Rwork0.1546 --
obs-22419 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.44 Å2 / Biso mean: 20.3547 Å2 / Biso min: 6.11 Å2
Refinement stepCycle: final / Resolution: 1.9→69.267 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1836 0 136 224 2196
Biso mean--22.59 24.28 -
Num. residues----221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062013
X-RAY DIFFRACTIONf_angle_d1.0142705
X-RAY DIFFRACTIONf_chiral_restr0.036280
X-RAY DIFFRACTIONf_plane_restr0.005329
X-RAY DIFFRACTIONf_dihedral_angle_d21.414826
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 (%)
1.9001-1.98660.26361380.198826212759100
1.9866-2.09130.19041380.171826202758100
2.0913-2.22230.19611400.155726602800100
2.2223-2.39390.21641390.159126372776100
2.3939-2.63490.20331400.160826542794100
2.6349-3.01610.21841400.155726562796100
3.0161-3.80.18581410.148626902831100
3.8-69.31280.18161440.13572761290599
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)
13.77731.8551-1.73624.0805-0.04274.4242-0.05020.14580.239-0.07150.02240.36930.1518-0.24080.01490.11190.0198-0.050.11160.0190.16134.2091-0.53811.0231
22.7098-1.96870.09832.7873-0.07210.5780.03710.02760.0485-0.1095-0.0098-0.02440.0476-0.0731-0.0270.0759-0.01410.00750.0784-0.01710.081126.1317-5.80132.5984
34.83991.21853.12231.17510.92772.69060.0571-0.0002-0.1716-0.07790.03010.09030.0604-0.0576-0.05820.1089-0.00380.00540.07080.00910.099213.0716-7.78285.0689
44.24691.1511-3.9495.09741.87345.48260.391-0.23560.01640.50820.0345-0.608-0.40890.5866-0.11160.1938-0.0016-0.01910.10620.00220.103730.74291.715414.0955
52.64832.4137-0.87462.554-0.50322.171-0.0368-0.12430.4132-0.05940.04490.2876-0.0526-0.24460.0080.13280.0167-0.0030.09490.00690.113311.78154.31969.8731
67.8182-0.66971.28713.70373.84157.2655-0.0126-0.1890.36350.20030.10870.8947-0.0058-0.94930.12640.1346-0.00360.08450.29340.08550.3938-2.507-3.700524.5265
72.9776-1.53163.29392.8296-0.37955.62130.0219-0.4291-0.24720.31280.20970.3910.315-0.4639-0.17140.2375-0.010.0550.17320.04750.15156.8514-10.46429.8598
82.37241.33391.01742.48571.00430.93290.0008-0.08180.03530.24090.03090.0387-0.0782-0.0514-0.01970.19060.02260.0070.10130.00380.075122.5319-1.301130.5376
94.4623-1.63720.12673.715-2.61593.0395-0.2035-0.4210.04380.6590.09520.4048-0.1458-0.4720.04310.27070.02290.09110.1893-0.03130.18777.65210.953831.7526
104.939-0.1471-0.34541.9812-0.23511.9531-0.0716-0.04960.14980.11720.09110.3546-0.0824-0.205-0.00340.16210.0122-0.00080.09820.01970.111411.52090.820322.3271
113.5206-3.8808-3.67224.72023.61114.2630.1759-0.1844-0.0041-0.1545-0.0507-0.50020.65240.58110.01010.24960.02570.01080.14040.01090.085529.7895-8.871420.7997
123.0017-1.32223.36522.8455-0.80794.4443-0.03190.07890.11570.11310.07530.43390.0531-0.2599-0.09790.1778-0.02270.0150.12380.06220.190510.3527-11.07220.0403
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 45 )A25 - 45
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 75 )A46 - 75
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 108 )A76 - 108
4X-RAY DIFFRACTION4chain 'A' and (resid 109 through 113 )A109 - 113
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 136 )A114 - 136
6X-RAY DIFFRACTION6chain 'B' and (resid 28 through 37 )B28 - 37
7X-RAY DIFFRACTION7chain 'B' and (resid 38 through 45 )B38 - 45
8X-RAY DIFFRACTION8chain 'B' and (resid 46 through 75 )B46 - 75
9X-RAY DIFFRACTION9chain 'B' and (resid 76 through 84 )B76 - 84
10X-RAY DIFFRACTION10chain 'B' and (resid 85 through 108 )B85 - 108
11X-RAY DIFFRACTION11chain 'B' and (resid 109 through 113 )B109 - 113
12X-RAY DIFFRACTION12chain 'B' and (resid 114 through 136 )B114 - 136

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