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- PDB-3uvd: Crystal Structure of the bromodomain of human Transcription activ... -

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Basic information

Entry
Database: PDB / ID: 3uvd
TitleCrystal Structure of the bromodomain of human Transcription activator BRG1 (SMARCA4) in complex with N-Methyl-2-pyrrolidone
ComponentsTranscription activator BRG1
KeywordsTRANSCRIPTION / Bromodomain / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and transcription activator / Protein BRG-1 / Protein brahma homolog 1 / SNF2-beta / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4 / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / GBAF complex ...positive regulation of glucose mediated signaling pathway / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / bBAF complex / neural retina development / npBAF complex / nBAF complex / negative regulation of androgen receptor signaling pathway / EGR2 and SOX10-mediated initiation of Schwann cell myelination / nucleosome array spacer activity / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / RNA polymerase I preinitiation complex assembly / RSC-type complex / ATP-dependent chromatin remodeler activity / regulation of nucleotide-excision repair / host-mediated activation of viral transcription / nucleosome disassembly / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of T cell differentiation / nuclear androgen receptor binding / positive regulation of double-strand break repair / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / positive regulation of signal transduction by p53 class mediator / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / ATP-dependent activity, acting on DNA / positive regulation of myoblast differentiation / Chromatin modifying enzymes / DNA polymerase binding / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / transcription coregulator binding / positive regulation of cell differentiation / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Formation of the beta-catenin:TCF transactivating complex / helicase activity / negative regulation of cell growth / kinetochore / positive regulation of miRNA transcription / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / RMTs methylate histone arginines / nuclear matrix / fibrillar center / p53 binding / transcription corepressor activity / nervous system development / positive regulation of cold-induced thermogenesis / histone binding / transcription coactivator activity / hydrolase activity / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular space / DNA binding / RNA binding / nucleoplasm / ATP binding / nucleus / membrane
Similarity search - Function
SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex ...SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / domain in helicases and associated with SANT domains / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Helicase conserved C-terminal domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
1-methylpyrrolidin-2-one / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsFilippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. ...Filippakopoulos, P. / Felletar, I. / Picaud, S. / Keates, T. / Muniz, J. / Gileadi, O. / 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 1.2Sep 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

Downloads & links

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Assembly

Deposited unit
A: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6592
Polymers14,5601
Non-polymers991
Water1,09961
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.200, 29.890, 67.060
Angle α, β, γ (deg.)90.000, 90.450, 90.000
Int Tables number4
Space group name H-MP1211
Detailsmonomer

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Components

#1: Protein Transcription activator BRG1 / BRG1-associated factor Protein BRG-1


Mass: 14559.822 Da / Num. of mol.: 1 / Fragment: unp residues 1448-1569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRG1 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-MB3 / 1-methylpyrrolidin-2-one


Mass: 99.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 28% MMW PEG smear 0.1M Tris.HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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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 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.52 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 4.2 / Number: 36801 / Rsym value: 0.067 / D res high: 1.85 Å / D res low: 29.89 Å / Num. obs: 10488 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.8529.8999.510.0580.0583.3
4.145.8510010.0530.0533.5
3.384.1410010.0590.0593.6
2.933.3810010.0710.0713.6
2.622.9310010.0710.0713.5
2.392.6210010.0860.0863.6
2.212.3910010.1130.1133.5
2.072.2110010.1690.1693.5
1.952.0710010.3040.3043.5
1.851.9510010.5440.5443.4
ReflectionResolution: 1.85→29.89 Å / Num. all: 10488 / Num. obs: 10488 / % possible obs: 100 % / Redundancy: 3.5 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.953.40.5441.4513615020.544100
1.95-2.073.50.3042.5495614230.304100
2.07-2.213.50.1694.2479113650.169100
2.21-2.393.50.1136443812630.113100
2.39-2.623.60.0867.7406611440.086100
2.62-2.933.50.0718.3379810700.071100
2.93-3.383.60.0718.233639410.071100
3.38-4.143.60.0598.828387900.059100
4.14-5.853.50.053922146250.053100
5.85-29.893.30.0587.112013650.05899.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.46 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.62 Å
Translation2.5 Å27.62 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Ensemble of PDB entries 2GRC, 2OSS, 2OUO, 2OO1, 3DAI, 3D7C, 3DWY, 3G0L, 3G0J, 3GG3

2grc

2oss

2ouo

2oo1

3dai

3d7c

3dwy

3g0l

3g0j

3gg3


Resolution: 1.85→29.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2907 / WRfactor Rwork: 0.2228 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7914 / SU B: 8.559 / SU ML: 0.132 / SU R Cruickshank DPI: 0.1611 / SU Rfree: 0.1607 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2624 502 4.8 %RANDOM
Rwork0.1996 ---
all0.2027 10482 --
obs0.2027 10479 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.18 Å2 / Biso mean: 46.1641 Å2 / Biso min: 18.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å2-0.82 Å2
2--2.13 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.85→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms990 0 7 61 1058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021012
X-RAY DIFFRACTIONr_bond_other_d0.0030.02732
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9991359
X-RAY DIFFRACTIONr_angle_other_deg1.0353.0011787
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8465121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18424.78346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.63915205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.259157
X-RAY DIFFRACTIONr_chiral_restr0.1040.2152
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211084
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02185
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 31 -
Rwork0.364 702 -
all-733 -
obs--100 %
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)
11.37380.9998-0.40030.734-0.29580.12130.0889-0.1224-0.06940.054-0.095-0.0233-0.00350.03530.00620.25020.10410.05350.25560.04650.171425.02025.330654.8682
21.4764-0.6275-1.02771.0409-0.60283.54820.13870.2127-0.1081-0.20960.04720.4091-0.1107-0.3601-0.18590.15390.0244-0.06130.2214-0.00330.27847.274714.551745.5281
32.4938-1.4982-0.00061.2434-0.37331.46480.19250.1805-0.0039-0.187-0.13020.07320.02260.0751-0.06230.11960.04430.02440.1683-0.02260.16118.119615.493647.2092
426.92654.668318.34421.17393.440412.68380.1836-1.8301-0.08420.06980.0603-0.20230.197-0.9278-0.24390.16590.12380.05450.7156-0.17240.126928.199817.626463.3937
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1447 - 1471
2X-RAY DIFFRACTION2A1472 - 1501
3X-RAY DIFFRACTION3A1502 - 1561
4X-RAY DIFFRACTION4A1562 - 1568

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