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- PDB-5hrw: Crystal structure of the fifth bromodomain of human PB1 in comple... -

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Basic information

Entry
Database: PDB / ID: 5hrw
TitleCrystal structure of the fifth bromodomain of human PB1 in complex with 1-propylisochromeno[3,4-c]pyrazol-5(2H)-one) compound
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / PBRM1 / BRG1-associated factor 180 / chromatin remodeling
Function / homology
Function and homology information


regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle ...regulation of G0 to G1 transition / regulation of nucleotide-excision repair / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / positive regulation of myoblast differentiation / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / kinetochore / RMTs methylate histone arginines / nuclear matrix / mitotic cell cycle / chromatin remodeling / negative regulation of cell population proliferation / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group ...Protein polybromo-1, Bromodomain 5 / Remodelling complex subunit Rsc/polybromo / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1-propylisochromeno[3,4-c]pyrazol-5(3H)-one / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTallant, C. / Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Newman, J.A. / Picaud, S. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Mikros, E. / Knapp, S.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery and Optimization of a Selective Ligand for the Switch/Sucrose Nonfermenting-Related Bromodomains of Polybromo Protein-1 by the Use of Virtual Screening and Hydration Analysis.
Authors: Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Tallant, C. / Hall, M.L. / Grigoriou, S. / Brownlee, P.M. / Fedorov, O. / Rogers, C. / Heidenreich, D. / Wanior, M. / Drosos, N. / Mexia, N. / ...Authors: Myrianthopoulos, V. / Gaboriaud-Kolar, N. / Tallant, C. / Hall, M.L. / Grigoriou, S. / Brownlee, P.M. / Fedorov, O. / Rogers, C. / Heidenreich, D. / Wanior, M. / Drosos, N. / Mexia, N. / Savitsky, P. / Bagratuni, T. / Kastritis, E. / Terpos, E. / Filippakopoulos, P. / Muller, S. / Skaltsounis, A.L. / Downs, J.A. / Knapp, S. / Mikros, E.
History
DepositionJan 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein polybromo-1
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,15910
Polymers29,2962
Non-polymers8638
Water1,45981
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2217
Polymers14,6481
Non-polymers5736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9383
Polymers14,6481
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.111, 59.101, 105.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein polybromo-1 / hPB1 / BRG1-associated factor 180 / BAF180 / Polybromo-1D / PB1 fifth bromodomain


Mass: 14648.000 Da / Num. of mol.: 2 / Fragment: UNP Residues 613-734
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PBRM1, BAF180, PB1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86U86
#2: Chemical ChemComp-64E / 1-propylisochromeno[3,4-c]pyrazol-5(3H)-one


Mass: 228.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N2O2
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M MES pH 6.5, 30% PEGMME5k
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9207 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9207 Å / Relative weight: 1
ReflectionResolution: 1.8→29.55 Å / Num. all: 23971 / Num. obs: 23971 / % possible obs: 97.4 % / Redundancy: 5 % / Rmerge(I) obs: 0.053 / Rsym value: 0.027 / Net I/σ(I): 18.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.735 / Mean I/σ(I) obs: 2.2 / % possible all: 93.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G0J

3g0j


Resolution: 1.8→29.55 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.817 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23573 1179 4.9 %RANDOM
Rwork0.20213 ---
obs0.20377 22752 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å2-0 Å20 Å2
2--0.28 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.8→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 59 81 1936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.021885
X-RAY DIFFRACTIONr_bond_other_d0.0040.021811
X-RAY DIFFRACTIONr_angle_refined_deg1.9312.0122530
X-RAY DIFFRACTIONr_angle_other_deg1.1953.0044166
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.77223.93389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6515358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6911515
X-RAY DIFFRACTIONr_chiral_restr0.1260.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212041
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02412
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4212.05870
X-RAY DIFFRACTIONr_mcbond_other1.4212.048869
X-RAY DIFFRACTIONr_mcangle_it2.143.061084
X-RAY DIFFRACTIONr_mcangle_other2.1393.0621085
X-RAY DIFFRACTIONr_scbond_it2.3282.4131015
X-RAY DIFFRACTIONr_scbond_other2.3172.41011
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6993.451441
X-RAY DIFFRACTIONr_long_range_B_refined5.64217.1032257
X-RAY DIFFRACTIONr_long_range_B_other5.5616.9962239
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.797→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 90 -
Rwork0.272 1584 -
obs--93.99 %
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
11.54210.30740.03390.0976-0.13210.57550.00650.216-0.05060.01320.0486-0.0059-0.0254-0.0525-0.0550.01310.0025-0.00190.0978-0.00590.056Chain A5.8543-10.4014-13.1927
20.0532-0.01590.28621.49050.22891.6135-0.05240.0522-0.00070.11920.03960.0373-0.25270.2810.01280.0783-0.0480.00070.0722-0.0150.0146Chain B17.843510.9704-8.1298
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A655 - 762
2X-RAY DIFFRACTION2B655 - 762

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