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- PDB-3uv2: Crystal structure of the bromodomain of human nucleosome-remodeli... -

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Basic information

Entry
Database: PDB / ID: 3uv2
TitleCrystal structure of the bromodomain of human nucleosome-remodeling factor subunit BPTF
Componentsbromodomain of human nucleosome-remodeling factor subunit BPTF
KeywordsTRANSCRIPTION / Bromodomain / BPTF / FALZ / FAC1 / Bromodomain and PHD finger-containing transcription factor / Fetal Alz-50 clone 1 protein / Fetal Alzheimer antigen / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding ...NURF complex / endoderm development / anterior/posterior pattern specification / ATPase complex / embryonic placenta development / methylated histone binding / cellular response to nerve growth factor stimulus / brain development / cell body / sequence-specific DNA binding / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / dendrite / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / extracellular exosome / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. ...Nucleosome-remodeling factor subunit BPTF / DDT domain / DDT domain / WHIM2 domain / Williams-Beuren syndrome DDT (WSD), D-TOX E motif / DDT domain profile. / domain in different transcription and chromosome remodeling factors / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Bromodomain-like / Histone Acetyltransferase; Chain A / Zinc finger, FYVE/PHD-type / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7PE / Nucleosome-remodeling factor subunit BPTF
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsFilippakopoulos, P. / Picaud, S. / Keates, T. / 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
DepositionNov 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Jan 31, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Sep 13, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: bromodomain of human nucleosome-remodeling factor subunit BPTF
A: 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1252
Polymers14,8151
Non-polymers3101
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)27.141, 66.809, 39.259
Angle α, β, γ (deg.)90.000, 106.160, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein bromodomain of human nucleosome-remodeling factor subunit BPTF / Bromodomain and PHD finger-containing transcription factor


Mass: 14814.816 Da / Num. of mol.: 1 / Fragment: unp residues 2914-3037
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BPTF, FAC1, FALZ / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q12830
#2: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT / Polyethylene glycol


Mass: 310.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.31 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.10M Na/KPO4, 20.0% PEG 3350, 10.0% EtGly, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionRedundancy: 3.7 % / Av σ(I) over netI: 12.9 / Number: 63353 / Rsym value: 0.05 / D res high: 1.58 Å / D res low: 20.551 Å / Num. obs: 17223 / % possible obs: 93.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
520.5597.910.0210.0213.6
3.53599.510.0210.0213.7
2.883.5398.110.0310.0313.8
2.52.8897.710.040.043.7
2.232.596.810.0520.0523.7
2.042.2395.710.0730.0733.7
1.892.0494.810.1230.1233.7
1.771.8993.710.1940.1943.7
1.671.7792.710.3330.3333.7
1.581.6779.510.5180.5183.4
ReflectionResolution: 1.58→25 Å / Num. all: 18460 / Num. obs: 17223 / % possible obs: 93.3 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.58-1.673.40.5181.5707421020.51879.5
1.67-1.773.70.3332.3875123580.33392.7
1.77-1.893.70.1944831422390.19493.7
1.89-2.043.70.1236.1792121240.12394.8
2.04-2.233.70.0739.9728019540.07395.7
2.23-2.53.70.05214.1677818140.05296.8
2.5-2.883.70.0417.3597415950.0497.7
2.88-3.533.80.03121.2512913660.03198.1
3.53-53.70.02130.6399210790.02199.5
5-20.5513.60.0212621405920.02197.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.33 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å20.55 Å
Translation2.5 Å20.55 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of 2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3DAI

2nxb

2oo1

2oss

2ouo

2rfj

3dai


Resolution: 1.58→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.948 / WRfactor Rfree: 0.1957 / WRfactor Rwork: 0.1488 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8933 / SU B: 2.9 / SU ML: 0.053 / SU R Cruickshank DPI: 0.088 / SU Rfree: 0.0946 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.209 881 5.1 %RANDOM
Rwork0.1623 ---
all0.1647 18457 --
obs0.1647 17222 93.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.14 Å2 / Biso mean: 18.3808 Å2 / Biso min: 7.35 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.59 Å2
2---0.51 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.58→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 10 204 1197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021058
X-RAY DIFFRACTIONr_bond_other_d0.0010.02761
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9831427
X-RAY DIFFRACTIONr_angle_other_deg0.9573.0021834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9675120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.2523.70454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55315193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.842158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211135
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02221
LS refinement shellResolution: 1.58→1.621 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.488 44 -
Rwork0.499 864 -
all-908 -
obs--68.74 %
Refinement TLS params.Method: refined / Origin x: 10.9029 Å / Origin y: 11.9298 Å / Origin z: 7.5454 Å
111213212223313233
T0.0387 Å20.0017 Å20.0099 Å2-0.0581 Å20.0007 Å2--0.0409 Å2
L0.2498 °2-0.0774 °2-0.0824 °2-0.8681 °20.0109 °2--0.197 °2
S-0.0036 Å °-0.0048 Å °0.0049 Å °-0.0021 Å °0.0201 Å °0.0045 Å °-0.0072 Å °-0.009 Å °-0.0165 Å °

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