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

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Basic information

Entry
Database: PDB / ID: 7mrh
TitleCrystal structure of the first bromodomain (BD1) of human BRDT bound to NC-II-259
ComponentsBromodomain testis-specific protein
KeywordsGENE REGULATION / BRDT / BRD / BET / contraceptive / cancer
Function / homology
Function and homology information


sperm DNA condensation / male meiotic nuclear division / regulation of RNA splicing / male meiosis I / histone H4 reader activity / : / RNA splicing / mRNA processing / histone binding / transcription coactivator activity ...sperm DNA condensation / male meiotic nuclear division / regulation of RNA splicing / male meiosis I / histone H4 reader activity / : / RNA splicing / mRNA processing / histone binding / transcription coactivator activity / chromatin remodeling / protein serine/threonine kinase activity / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / 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-like ...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-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-ZMJ / Bromodomain testis-specific protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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)27,3244
Polymers26,6392
Non-polymers6852
Water3,027168
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-14 kcal/mol
Surface area11630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.640, 29.820, 73.220
Angle α, β, γ (deg.)90.000, 98.560, 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
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-ZMJ / N-[3-(2-methyl-1-oxo-1,2-dihydroisoquinolin-4-yl)phenyl]ethanesulfonamide


Mass: 342.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium citrate tribasic pH 7.0, 20% 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: Jul 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→33.93 Å / Num. obs: 19605 / % possible obs: 96.4 % / Redundancy: 3.292 % / Biso Wilson estimate: 28.65 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.085 / Χ2: 0.959 / Net I/σ(I): 11.23 / Num. measured all: 64537 / Scaling rejects: 70
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
1.98-2.033.3240.5553.054780146714380.7610.66198
2.03-2.093.2860.4653.64604144414010.8240.55797
2.09-2.153.2530.3534.584470143013740.8950.42596.1
2.15-2.213.1550.2935.414029133512770.9120.35695.7
2.21-2.292.8770.2116.413585135612460.9470.26191.9
2.29-2.373.2770.2166.764021126712270.9530.26196.8
2.37-2.463.5390.1688.634293124512130.9680.19997.4
2.46-2.563.4910.1359.634116119911790.9840.16198.3
2.56-2.673.4830.10111.563929115311280.9880.12197.8
2.67-2.83.4710.09112.773770110610860.9880.10998.2
2.8-2.953.4850.08414.083576105710260.9890.09997.1
2.95-3.133.3520.07515.0531749829470.9910.08996.4
3.13-3.353.3330.06116.7830639599190.9920.07395.8
3.35-3.623.2940.05419.2826658538090.9940.06594.8
3.62-3.963.10.04520.6224468177890.9940.05596.6
3.96-4.432.7650.04420.518947466850.9940.05491.8
4.43-5.113.3530.04322.9521366566370.9950.05197.1
5.11-6.263.360.04122.6418385615470.9960.04997.5
6.26-8.863.2820.04323.0114214484330.9980.05196.7
8.86-33.932.980.03422.957272662440.9980.04291.7

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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: 1.98→33.93 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1099 5.61 %
Rwork0.1716 18502 -
obs0.1743 19601 96.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.71 Å2 / Biso mean: 36.6971 Å2 / Biso min: 17.43 Å2
Refinement stepCycle: final / Resolution: 1.98→33.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1806 0 48 168 2022
Biso mean--24.92 40.72 -
Num. residues----218
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 (%)
1.98-2.070.29551350.23882273240898
2.07-2.180.24731360.20482283241996
2.18-2.320.22141320.18472227235994
2.32-2.490.28651390.18912333247298
2.49-2.750.27051390.19342345248498
2.75-3.140.24671370.19552314245197
3.14-3.960.20371390.15482326246596
3.96-33.930.16681420.14262401254395
Refinement TLS params.Method: refined / Origin x: -11.2117 Å / Origin y: 2.0769 Å / Origin z: -21.6515 Å
111213212223313233
T0.2409 Å2-0.0025 Å2-0.0045 Å2-0.2148 Å20.0031 Å2--0.2322 Å2
L1.0288 °20.2107 °20.0581 °2-0.6832 °20.0572 °2--0.2651 °2
S0.0306 Å °-0.1174 Å °-0.0021 Å °0.2134 Å °-0.0308 Å °0.0123 Å °0.0187 Å °0.0002 Å °0.0106 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA28 - 136
2X-RAY DIFFRACTION1allB28 - 136
3X-RAY DIFFRACTION1allC1 - 2
4X-RAY DIFFRACTION1allS1 - 168

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