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- PDB-5ii1: Crystal Structure of the fifth bromodomain of human polybromo (PB... -

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Basic information

Entry
Database: PDB / ID: 5ii1
TitleCrystal Structure of the fifth bromodomain of human polybromo (PB1) in complex with 1-methylisochromeno[3,4-c]pyrazol-5(3H)-one
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / bromodomain / complex / small molecule / structural genomics consortium / SGC
Function / homology
Function and homology information


regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of double-strand break repair / 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 / RSC-type complex / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear chromosome / positive regulation of double-strand break repair / 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 / regulation of transcription by RNA polymerase II / chromatin / 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 / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1-methyl[2]benzopyrano[3,4-c]pyrazol-5(3H)-one / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Felletar, I. / Myrianthopoulos, V. / Mikros, E. / von Delft, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust095751/Z/11/Z United Kingdom
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
DepositionMar 1, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Database references
Revision 1.3Jan 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,6964
Polymers29,2962
Non-polymers4002
Water1,982110
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8482
Polymers14,6481
Non-polymers2001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8482
Polymers14,6481
Non-polymers2001
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.110, 57.970, 106.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 653 - 762 / Label seq-ID: 11 - 120

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 14648.000 Da / Num. of mol.: 2
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 BL21(DE3) (bacteria) / Variant (production host): R3 / References: UniProt: Q86U86
#2: Chemical ChemComp-6BL / 1-methyl[2]benzopyrano[3,4-c]pyrazol-5(3H)-one


Mass: 200.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H8N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.1
Details: 18% PEG_3350 0.15M Na_malonate_pH7.0 10v/v ethylene_glycol 0.1M bis_tris_propane pH 8.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.52 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionResolution: 2.015→22.275 Å / Num. obs: 17373 / % possible obs: 99.8 % / Redundancy: 4.3 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/av σ(I): 8.107 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.02-2.124.30.6711.21100
2.12-2.254.20.3981.91100
2.25-2.414.30.2692.91100
2.41-2.64.30.1884.11100
2.6-2.854.30.1146.5199.9
2.85-3.194.30.0749.9199.7
3.19-3.684.40.0513.5199.8
3.68-4.514.50.03417.7199.8
4.51-6.374.40.02821.8199.9
6.37-22.27540.0359.4195.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 53.9 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å22.27 Å
Translation2.5 Å22.27 Å

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
SCALA3.3.16data scaling
PHASER2.1.4phasing
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 3MB4,3DAI,3HMH,2GRC,2OSS,2OUO,3D7C,3DWY

3mb4

3dai

3hmh

2grc

2oss

2ouo

3d7c

3dwy


Resolution: 2.02→22.275 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.918 / SU B: 10.014 / SU ML: 0.137 / SU R Cruickshank DPI: 0.1845 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.181
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 876 5.1 %RANDOM
Rwork0.1879 ---
obs0.1911 16456 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 117.58 Å2 / Biso mean: 38.054 Å2 / Biso min: 17.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å2-0 Å2
2--0.22 Å20 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 2.02→22.275 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1820 0 30 110 1960
Biso mean--28.48 41.06 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191895
X-RAY DIFFRACTIONr_bond_other_d0.0070.021768
X-RAY DIFFRACTIONr_angle_refined_deg1.6112.0012563
X-RAY DIFFRACTIONr_angle_other_deg1.4433.0014044
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5115223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38423.84691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98215348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8391515
X-RAY DIFFRACTIONr_chiral_restr0.0910.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212099
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02418
X-RAY DIFFRACTIONr_mcbond_it6.0515.153892
X-RAY DIFFRACTIONr_mcbond_other6.0325.148891
X-RAY DIFFRACTIONr_mcangle_it6.4959.6221112
Refine LS restraints NCS

Ens-ID: 1 / Number: 12004 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.015→2.067 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 80 -
Rwork0.296 1179 -
all-1259 -
obs--100 %
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)
10.011-0.128-0.09612.11940.66552.3659-0.0155-0.0129-0.0026-0.1199-0.0030.05130.0880.2470.01850.11790.0397-0.00330.0828-0.00840.003138.003317.58768.6735
21.2428-0.435-0.39350.3939-0.25440.76540.0464-0.06530.0131-0.01220.01830.034-0.00360.0187-0.06470.0826-0.0238-0.0080.07940.00160.043526.654939.601513.5646
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A652 - 763
2X-RAY DIFFRACTION2B653 - 763

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