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- PDB-3k2j: Crystal Structure of the 3rd Bromodomain of Human Poly-bromodomai... -

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Basic information

Entry
Database: PDB / ID: 3k2j
TitleCrystal Structure of the 3rd Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)
ComponentsProtein polybromo-1
KeywordsTRANSCRIPTION / PB1 / polybromo 1 isoform 1 / BAF180 / Polybromo01D / PBRM1 / BRG1-associated factor 180 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of G0 to G1 transition / RSC-type complex / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / 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 / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / Chaikuad, A. / Pike, A.C.W. / Krojer, T. / Sethi, R. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. ...Filippakopoulos, P. / Picaud, S. / Keates, T. / Chaikuad, A. / Pike, A.C.W. / Krojer, T. / Sethi, R. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal Structure of the 3rd Bromodomain of Human Poly-bromodomain containing protein 1 (PB1)
Authors: Filippakopoulos, P. / Picaud, S. / Keates, T. / Chaikuad, A. / Pike, A.C.W. / Krojer, T. / Sethi, R. / von Delft, F. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Bountra, C. / Knapp, S.
History
DepositionSep 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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_ncs_dom_lim / 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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)31,5036
Polymers31,2402
Non-polymers2634
Water97354
1
A: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6913
Polymers15,6201
Non-polymers712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein polybromo-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8123
Polymers15,6201
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint-9 kcal/mol
Surface area13590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.390, 81.390, 79.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 2 / Auth seq-ID: 346 - 459 / Label seq-ID: 14 - 127

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe protein is monomeric by gel filtration.

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Components

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


Mass: 15619.836 Da / Num. of mol.: 2 / Fragment: Bromo 3 domain, UNP residues 388-494
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PB1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q86U86
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.43 % / Mosaicity: 0.23 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M NaOAc.3H20 pH 5.5, 1.1M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→36.221 Å / Num. all: 15266 / Num. obs: 15266 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 50.8 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 14.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.744 / Mean I/σ(I) obs: 2 / Num. unique all: 2231 / Rsym value: 0.744 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 35.59 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å36.22 Å
Translation2.5 Å36.22 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 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI, 3D7C, 3DWY

2nxb

2oo1

2oss

2ouo

2rfj

3dai

3d7c

3dwy


Resolution: 2.2→36.22 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.278 / WRfactor Rwork: 0.233 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.799 / SU B: 16.939 / SU ML: 0.191 / SU R Cruickshank DPI: 0.281 / SU Rfree: 0.225 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.281 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27 744 4.9 %RANDOM
Rwork0.224 ---
all0.227 15252 --
obs0.227 15238 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.22 Å2 / Biso mean: 33.606 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20.87 Å20 Å2
2--1.74 Å20 Å2
3----2.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1891 0 12 54 1957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211994
X-RAY DIFFRACTIONr_bond_other_d0.0020.021322
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9722709
X-RAY DIFFRACTIONr_angle_other_deg0.9433217
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0425254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.30325.4100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.82815331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1631510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212275
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02383
X-RAY DIFFRACTIONr_mcbond_it3.10531260
X-RAY DIFFRACTIONr_mcbond_other2.0513496
X-RAY DIFFRACTIONr_mcangle_it3.82651996
X-RAY DIFFRACTIONr_scbond_it6.0278734
X-RAY DIFFRACTIONr_scangle_it6.46311711
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
703TIGHT POSITIONAL0.020.05
853MEDIUM POSITIONAL0.020.5
703TIGHT THERMAL0.10.5
853MEDIUM THERMAL0.082
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 51 -
Rwork0.297 1069 -
all-1120 -
obs--99.56 %
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)
14.8668-0.27920.85896.7969-0.66915.8078-0.0427-0.34910.22750.14380.17110.311-0.1657-0.4301-0.12840.037-0.05820.01610.232-0.01930.031520.4899-25.75464.2524
22.27011.04590.56049.1508-3.59153.6913-0.21680.0277-0.14670.15950.0536-0.67610.0876-0.00330.16320.107-0.03510.0210.0931-0.02830.083930.777-27.4642-0.0053
36.3824-1.2608-0.36965.24250.8455.54190.02740.05950.4007-0.33240.11380.0846-0.45720.0227-0.14120.1352-0.112-0.01090.13240.02340.036211.9032-30.5851-15.6784
49.5354-2.8903-3.88553.2692.52864.2897-0.0952-0.1317-0.6039-0.0823-0.11560.21720.09790.16240.21070.0737-0.0255-0.00430.12160.03510.05998.0124-40.1217-11.1754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A342 - 427
2X-RAY DIFFRACTION2A428 - 462
3X-RAY DIFFRACTION3B342 - 427
4X-RAY DIFFRACTION4B428 - 462

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