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- PDB-3iu6: Crystal structure of the sixth bromodomain of human poly-bromodom... -

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Basic information

Entry
Database: PDB / ID: 3iu6
TitleCrystal structure of the sixth bromodomain of human poly-bromodomain containing protein 1 (PB1)
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / PB1 / polybromo 1 isoform 1 / BAF180 / Polybromo0ID / PBRM1 / BRG1-associated factor 180 / Structural Genomics / SGC / Structural Genomics Consortium / Bromodomain / Chromatin regulator / DNA-binding / Nucleus / Phosphoprotein / Transcription regulation
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsFilippakopoulos, P. / Keates, T. / Picaud, S. / Pike, A.C.W. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. ...Filippakopoulos, P. / Keates, T. / Picaud, S. / Pike, A.C.W. / Ugochukwu, E. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: Cell(Cambridge,Mass.) / Year: 2012
Title: Histone recognition and large-scale structural analysis of the human bromodomain family.
Authors: Filippakopoulos, P. / Picaud, S. / Mangos, M. / Keates, T. / Lambert, J.P. / Barsyte-Lovejoy, D. / Felletar, I. / Volkmer, R. / Muller, S. / Pawson, T. / Gingras, A.C. / Arrowsmith, C.H. / Knapp, S.
History
DepositionAug 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 11, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7725
Polymers17,5211
Non-polymers2524
Water3,099172
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.400, 66.400, 85.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-950-

ZN

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Components

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


Mass: 17520.754 Da / Num. of mol.: 1 / Fragment: Bromo 6 domain: UNP residues 773-914
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PB1, PBRM1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q86U86
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.01M ZnCl2, 0.1M Tris-HCl pH 8.0, 20% PEG 6000, 10% Ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.79→33.2 Å / Num. all: 21260 / Num. obs: 21132 / % possible obs: 99.4 % / Redundancy: 8.4 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.136 / Rsym value: 0.136 / Net I/σ(I): 11.2
Reflection shellResolution: 1.79→1.88 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 2 / Num. unique all: 2932 / Rsym value: 0.87 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 58.92 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.2 Å
Translation2.5 Å33.2 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of PDB entries 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 1.79→33.2 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.159 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.903 / SU B: 3.958 / SU ML: 0.058 / SU R Cruickshank DPI: 0.094 / SU Rfree: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 1074 5.1 %RANDOM
Rwork0.165 ---
all0.167 21030 --
obs0.167 20982 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.45 Å2 / Biso mean: 10.665 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.34 Å2-0.17 Å20 Å2
2---0.34 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.79→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 13 172 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221251
X-RAY DIFFRACTIONr_bond_other_d0.0010.02873
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.9681687
X-RAY DIFFRACTIONr_angle_other_deg2.77732135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5145144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92824.65873
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70415238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2891511
X-RAY DIFFRACTIONr_chiral_restr0.0940.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02243
X-RAY DIFFRACTIONr_mcbond_it2.6583726
X-RAY DIFFRACTIONr_mcbond_other0.9243281
X-RAY DIFFRACTIONr_mcangle_it3.94751193
X-RAY DIFFRACTIONr_scbond_it6.4388525
X-RAY DIFFRACTIONr_scangle_it8.37311493
LS refinement shellResolution: 1.79→1.836 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 74 -
Rwork0.306 1401 -
all-1475 -
obs--97.04 %
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)
12.6876-0.7202-1.89791.83820.08024.3158-0.1823-0.0262-0.1535-0.00450.0119-0.02530.2637-0.05680.17040.1216-0.0163-0.02370.0442-0.00780.064934.2417.48910.235
211.83412.61130.65643.8870.3492.8158-0.0284-0.57140.13750.4248-0.0077-0.2459-0.1320.38760.03610.16590.0202-0.0610.1118-0.01420.085543.1768.39822.361
33.20190.553-1.20821.7666-0.0371.83160.0450.02890.3354-0.05690.0608-0.0919-0.21690.073-0.10580.1121-0.0067-0.00270.0384-0.01640.087539.05419.90812.988
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A740 - 774
2X-RAY DIFFRACTION2A775 - 801
3X-RAY DIFFRACTION3A802 - 882

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