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- PDB-5ii2: Crystal Structure of the fifth bromodomain of human polybromo (PB... -

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Basic information

Entry
Database: PDB / ID: 5ii2
TitleCrystal Structure of the fifth bromodomain of human polybromo (PB1) in complex with 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-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 T cell differentiation / positive regulation of double-strand break repair / 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 T cell differentiation / positive regulation of double-strand break repair / 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 / 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 / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
CITRIC ACID / : / Chem-LU2 / Protein polybromo-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)30,1397
Polymers29,2962
Non-polymers8435
Water3,279182
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1654
Polymers14,6481
Non-polymers5173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9733
Polymers14,6481
Non-polymers3252
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.520, 58.510, 138.230
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 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-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-LU2 / 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4H-chromen-4-one / Luteolin


Mass: 286.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.20M K3(cit) 0.1M BTProp pH 7.5 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: Apr 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionResolution: 2.1→24.186 Å / Num. obs: 20237 / % possible obs: 99 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/av σ(I): 3.929 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.215.90.3682195.3
2.21-2.355.80.2732.7198.4
2.35-2.5160.2263.2199.8
2.51-2.716.20.1843.81100
2.71-2.976.60.163.91100
2.97-3.326.80.1553.71100
3.32-3.836.90.11651100
3.83-4.76.90.0767.41100
4.7-6.646.70.0727.71100
6.64-24.1866.10.0724.2198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å24.19 Å
Translation2.1 Å24.19 Å

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHASER2.5.7phasing
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: 2.1→24.186 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.205 / SU ML: 0.105 / SU R Cruickshank DPI: 0.1658 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.162
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1042 5.2 %RANDOM
Rwork0.1735 ---
obs0.1762 19140 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 82.33 Å2 / Biso mean: 28.073 Å2 / Biso min: 14.17 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.67 Å2-0 Å2
3----1.23 Å2
Refinement stepCycle: final / Resolution: 2.1→24.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 57 182 2110
Biso mean--22.88 33.88 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191972
X-RAY DIFFRACTIONr_bond_other_d0.0020.021835
X-RAY DIFFRACTIONr_angle_refined_deg1.6232.0182664
X-RAY DIFFRACTIONr_angle_other_deg0.9993.0014214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61323.93694
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34615368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6961515
X-RAY DIFFRACTIONr_chiral_restr0.0950.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212180
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_mcbond_it2.4173.854911
X-RAY DIFFRACTIONr_mcbond_other2.3463.85910
X-RAY DIFFRACTIONr_mcangle_it3.1537.1541135
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 77 -
Rwork0.203 1304 -
all-1381 -
obs--94.27 %
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)
10.208-0.0726-0.34430.49630.1440.80040.03350.0049-0.034-0.0026-0.02910.0098-0.137-0.0388-0.00440.07620.00660.0070.07170.01380.02184.632-5.4916-22.5511
20.1308-0.01720.27510.40270.21710.78210.02060.00660.0110.0281-0.0179-0.00010.10770.0173-0.00270.0722-0.0024-0.01540.069-0.01340.015315.5826-28.2683-20.3152
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A652 - 766
2X-RAY DIFFRACTION2B652 - 764

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