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- PDB-7mrc: Crystal structure of the first bromodomain (BD1) of human BRDT bo... -

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Basic information

Entry
Database: PDB / ID: 7mrc
TitleCrystal structure of the first bromodomain (BD1) of human BRDT bound to GXH-II-052
ComponentsBromodomain testis-specific protein
KeywordsGENE REGULATION / BRDT / BRD / BET / contraceptive / cancer
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / localization / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding ...sperm DNA condensation / male meiotic nuclear division / male meiosis I / regulation of RNA splicing / localization / histone reader activity / RNA splicing / lysine-acetylated histone binding / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / 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-ZMS / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsChan, A. / 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)1U54HD093540 United States
CitationJournal: J.Med.Chem. / Year: 2022
Title: Bivalent BET Bromodomain Inhibitors Confer Increased Potency and Selectivity for BRDT via Protein Conformational Plasticity.
Authors: Guan, X. / Cheryala, N. / Karim, R.M. / Chan, A. / Berndt, N. / Qi, J. / Georg, G.I. / Schonbrunn, E.
History
DepositionMay 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: 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 1.2Aug 24, 2022Group: 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 18, 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

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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)28,3949
Polymers26,6392
Non-polymers1,7557
Water2,810156
1
A: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5064
Polymers13,3191
Non-polymers1863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Bromodomain testis-specific protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8885
Polymers13,3191
Non-polymers1,5694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.360, 34.890, 110.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRDT / Plasmid: pLIC-His / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q58F21
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZMS / N,N'-{oxybis[(ethane-2,1-diyl)oxy(1-oxoethane-2,1-diyl)piperidine-1,4-diyl]}bis{4-[(4-{4-chloro-3-[(2-methylpropane-2-sulfonyl)amino]anilino}-5-methylpyrimidin-2-yl)amino]-2-fluorobenzamide}


Mass: 1366.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H76Cl2F2N14O11S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.26 Å3/Da / Density % sol: 45.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→30.448 Å / Num. obs: 35015 / % possible obs: 97.4 % / Redundancy: 6.63 % / Biso Wilson estimate: 19.97 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.042 / Χ2: 1.024 / Net I/σ(I): 25.58 / Num. measured all: 232153 / Scaling rejects: 83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.597.120.36.8817885263625120.9750.32395.3
1.59-1.636.9740.2537.9617233251824710.980.27398.1
1.63-1.686.9410.1929.8916734249224110.9890.20896.7
1.68-1.736.8960.16111.6116282242623610.9910.17497.3
1.73-1.796.7710.12114.6515520233322920.9940.13198.2
1.79-1.856.6580.10116.9314641226121990.9950.1197.3
1.85-1.926.4240.08119.6813921219221670.9970.08898.9
1.92-25.9660.06422.6511831211019830.9970.07194
2-2.096.6290.05727.912867202619410.9970.06195.8
2.09-2.196.9080.04833.0913318196419280.9980.05298.2
2.19-2.316.770.04335.9712552186318540.9980.04799.5
2.31-2.456.8430.04137.9711709173517110.9990.04598.6
2.45-2.626.640.04139.8710950166716490.9990.04498.9
2.62-2.836.5240.03741.5410067155315430.9990.0499.4
2.83-3.16.3190.03442.818985143414220.9990.03799.2
3.1-3.475.8820.03243.417646131313000.9990.03599
3.47-45.860.02944.626259116310680.9990.03291.8
4-4.96.5120.02948.8464479969900.9990.03199.4
4.9-6.936.3040.03147.5650127997950.9990.03399.5
6.93-30.4485.4880.0343.9322944714180.9970.03488.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.11.1-2575_2829refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCX

4kcx


Resolution: 1.55→30.448 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1954 1197 3.42 %
Rwork0.173 33815 -
obs0.1738 35012 97.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 191.68 Å2 / Biso mean: 31.1108 Å2 / Biso min: 9.67 Å2
Refinement stepCycle: final / Resolution: 1.55→30.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1849 0 117 156 2122
Biso mean--26.79 34.69 -
Num. residues----224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062089
X-RAY DIFFRACTIONf_angle_d1.0282832
X-RAY DIFFRACTIONf_chiral_restr0.044284
X-RAY DIFFRACTIONf_plane_restr0.006353
X-RAY DIFFRACTIONf_dihedral_angle_d10.9351949
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.55-1.61210.2341300.1914366397
1.6121-1.68550.24711300.1814368797
1.6855-1.77430.21151310.1789369597
1.7743-1.88550.17461330.1745374498
1.8855-2.0310.20881290.1732363995
2.031-2.23530.16361330.1675377798
2.2353-2.55870.19081350.1785379899
2.5587-3.22310.20371370.1835387699
3.2231-30.4480.19351390.1635393696
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)
16.52470.39020.32944.63530.51940.0704-0.15660.79870.0171-0.36010.22220.76160.0744-0.43540.41780.1765-0.1395-0.0240.51010.12730.3815-15.9037-18.0867-21.0685
21.65470.67531.92581.13092.0954.86420.1209-0.1633-0.35210.71570.06570.35930.4116-0.3238-0.25960.2571-0.05040.04880.23470.01770.1641-5.6621-16.1614-12.0755
32.24561.78890.79321.96110.53170.94490.0417-0.02790.04010.3957-0.0170.0986-0.0388-0.04050.01720.24940.00190.01630.169-0.00570.14183.1831-1.6427-10.5416
41.7767-0.0716-0.25251.559-0.02611.4862-0.12350.05060.0408-0.04150.21120.3476-0.1632-0.42140.04010.14120.0264-0.03010.21210.05050.1563-5.2493-4.521-21.0836
55.1619-2.9888-0.69382.2938-0.53111.6369-0.10280.4402-0.3231-0.1587-0.3706-1.1431-0.03731.02530.41370.19190.04720.02330.30440.03950.321614.3474-4.4937-19.9389
64.08851.39181.35845.36991.93113.1630.02350.1917-0.2233-0.18290.0692-0.05750.328-0.2159-0.06130.1968-0.0259-0.02180.12940.02240.08320.1229-17.8255-20.5953
70.5192-0.00890.81250.51140.3191.70140.2178-1.77160.09071.7449-0.3542-0.4252-0.0644-0.34680.16230.9361-0.31230.14731.07180.1450.903941.4821-29.1306-10.8732
82.0785-1.3584-0.1314.32710.70061.09180.00320.036-0.07350.1471-0.0184-0.16690.02840.0830.04360.1415-0.0115-0.03320.1571-0.00150.139725.1848-18.507-7.2732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 37 )A25 - 37
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 45 )A38 - 45
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 65 )A46 - 65
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 108 )A66 - 108
5X-RAY DIFFRACTION5chain 'A' and (resid 109 through 113 )A109 - 113
6X-RAY DIFFRACTION6chain 'A' and (resid 114 through 136 )A114 - 136
7X-RAY DIFFRACTION7chain 'B' and (resid 25 through 29 )B25 - 29
8X-RAY DIFFRACTION8chain 'B' and (resid 30 through 136 )B30 - 136

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