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

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Basic information

Entry
Database: PDB / ID: 5iid
TitleCrystal Structure of the fifth bromodomain of human polybromo (PB1) in complex with 2-(3,4-dihydroxyphenyl)-5-hydroxy-4H-chromen-4-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 / regulation of nucleotide-excision repair / RSC-type complex / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / 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 / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / 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 / transcription elongation by RNA polymerase II / positive regulation of cell differentiation / 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 (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / 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 (BAH) domain superfamily / Bromo adjacent homology domain / Bromo adjacent homology (BAH) domain / BAH domain / 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
Chem-6BK / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Felletar, I. / von Delft, F. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S.
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 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id
Revision 1.4Jan 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)29,8364
Polymers29,2962
Non-polymers5402
Water88349
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9182
Polymers14,6481
Non-polymers2701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9182
Polymers14,6481
Non-polymers2701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.500, 56.400, 139.480
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: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 652 - 766 / Label seq-ID: 10 - 124

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-6BK / 2-(3,4-dihydroxyphenyl)-5-hydroxy-4H-1-benzopyran-4-one


Mass: 270.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.79 Å3/Da / Density % sol: 55.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.20M Na2SO4 0.1M BTProp pH 8.5 20.0% PEG 3350 10.0% EtGly

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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: Jul 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionResolution: 2.4→18.632 Å / Num. obs: 13364 / % possible obs: 99.3 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/av σ(I): 6.941 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.4-2.533.50.7841197
2.53-2.684.90.6141.31100
2.68-2.874.90.4161.91100
2.87-3.14.90.2473.11100
3.1-3.394.90.1584.81100
3.39-3.794.90.17.41100
3.79-4.384.90.05712.51100
4.38-5.374.80.04416.51100
5.37-7.594.60.04714.61100
7.59-18.63240.02424.1192.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.71 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å18.63 Å
Translation2.5 Å18.63 Å

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Processing

Software
NameVersionClassification
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMAC5.6.0117refinement
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: 2.4→18.6 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 18.795 / SU ML: 0.216 / SU R Cruickshank DPI: 0.3449 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.345 / ESU R Free: 0.273
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2817 659 4.9 %RANDOM
Rwork0.2175 ---
obs0.2207 12658 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 124.12 Å2 / Biso mean: 38.291 Å2 / Biso min: 19.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2--2.5 Å20 Å2
3----2.84 Å2
Refinement stepCycle: final / Resolution: 2.4→18.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1894 0 40 49 1983
Biso mean--45.64 41.39 -
Num. residues----230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221972
X-RAY DIFFRACTIONr_bond_other_d0.0040.021364
X-RAY DIFFRACTIONr_angle_refined_deg1.4712.012658
X-RAY DIFFRACTIONr_angle_other_deg1.1673.0013298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3785228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06423.95896
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60915374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1851516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212146
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02384
Refine LS restraints NCS

Ens-ID: 1 / Number: 4275 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.609 24 -
Rwork0.345 778 -
all-802 -
obs--92.18 %
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)
11.003-0.46331.3320.6722-0.75043.32410.023-0.02830.06760.0477-0.08110.04610.2781-0.02010.05810.0885-0.0125-0.01660.08920.02860.08574.445933.168922.3153
20.4639-0.2739-0.64630.91580.25142.22430.0619-0.1447-0.0431-0.0785-0.0528-0.087-0.30920.1066-0.00910.1004-0.02960.01080.14380.00210.081915.877755.924620.3843
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A653 - 766
2X-RAY DIFFRACTION2B652 - 765

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