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

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Basic information

Entry
Database: PDB / ID: 7mrg
TitleCrystal structure of the first bromodomain (BD1) of human BRDT bound to NC-II-153
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-ZMM / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 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 1.2Oct 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)27,4357
Polymers26,6392
Non-polymers7965
Water3,189177
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-13 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.870, 66.620, 142.720
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) / References: UniProt: Q58F21
#2: Chemical ChemComp-ZMM / 2-methyl-4-[3-(2-oxopyrrolidin-1-yl)phenyl]isoquinolin-1(2H)-one


Mass: 318.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.67 Å3/Da / Density % sol: 53.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium sulfate, 0.1 M Sodium cacodylate trihydrate pH 6.5, 30% w/v Polyethylene glycol 8,000

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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: Apr 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→48.7 Å / Num. obs: 19986 / % possible obs: 98.1 % / Redundancy: 6.427 % / Biso Wilson estimate: 25.32 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.128 / Rrim(I) all: 0.139 / Χ2: 0.934 / Net I/σ(I): 8.67 / Num. measured all: 128444 / Scaling rejects: 14
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
1.99-2.046.7940.6923.089743145414340.8620.74998.6
2.04-2.16.6540.5653.629322142914010.910.61398
2.1-2.166.6010.4344.519149141613860.9390.47197.9
2.16-2.226.6190.3665.18783134913270.9630.39798.4
2.22-2.36.4330.2885.988665136613470.9730.31498.6
2.3-2.386.4430.2735.997906124412270.9730.29798.6
2.38-2.476.1560.2077.267640125512410.9840.22698.9
2.47-2.575.7770.1827.376314117110930.980.20193.3
2.57-2.686.4910.1569.127484117411530.9880.1798.2
2.68-2.816.8330.1399.97421109510860.9920.1599.2
2.81-2.976.7680.12610.867113105710510.990.13799.4
2.97-3.156.7550.11312.1365939839760.9920.12399.3
3.15-3.366.5140.10312.9361959599510.9920.11299.2
3.36-3.636.4340.113.7855658728650.9920.10899.2
3.63-3.986.2610.09114.4650098098000.9950.09998.9
3.98-4.455.8870.0914.5244277667520.9920.09998.2
4.45-5.145.4140.08713.7332976666090.9890.09691.4
5.14-6.296.3850.08514.3635825705610.9960.09298.4
6.29-8.96.1990.08114.8828084634530.9960.08897.8
8.9-48.75.2310.0814.1514282842730.9940.08796.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KCX

4kcx


Resolution: 1.99→48.7 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 999 5 %
Rwork0.2239 18979 -
obs0.2263 19978 98.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.69 Å2 / Biso mean: 31.7918 Å2 / Biso min: 16.42 Å2
Refinement stepCycle: final / Resolution: 1.99→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1805 0 57 177 2039
Biso mean--28.74 35.76 -
Num. residues----219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.99-2.090.35771390.28912632277198
2.09-2.230.25441400.24322659279998
2.23-2.40.28331410.22622676281799
2.4-2.640.29431390.22822646278596
2.64-3.020.29261450.2272758290399
3.02-3.810.27011460.20792764291099
3.81-48.70.23211490.2142844299396
Refinement TLS params.Method: refined / Origin x: 7.3806 Å / Origin y: -4.9163 Å / Origin z: 21.1565 Å
111213212223313233
T0.2085 Å2-0.0016 Å2-0.0179 Å2-0.2246 Å2-0.0078 Å2--0.2326 Å2
L1.1686 °20.4077 °2-0.0058 °2-1.3339 °2-0.0125 °2--0.4097 °2
S-0.0719 Å °0.2495 Å °-0.0368 Å °-0.1078 Å °0.0405 Å °-0.0104 Å °0.0014 Å °-0.0016 Å °0.0351 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA28 - 135
2X-RAY DIFFRACTION1allB26 - 136
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 180
5X-RAY DIFFRACTION1allE1 - 2
6X-RAY DIFFRACTION1allD1

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