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- PDB-5ea1: Crystal Structure of SMARCA4 bromodomain in complex with MPD -

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Basic information

Entry
Database: PDB / ID: 5ea1
TitleCrystal Structure of SMARCA4 bromodomain in complex with MPD
ComponentsTranscription activator BRG1
KeywordsTRANSCRIPTION / four helical bundle
Function / homology
Function and homology information


positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / neural retina development / GBAF complex / regulation of G0 to G1 transition / Tat protein binding ...positive regulation of glucose mediated signaling pathway / bBAF complex / npBAF complex / nBAF complex / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of androgen receptor signaling pathway / neural retina development / GBAF complex / regulation of G0 to G1 transition / Tat protein binding / nucleosome disassembly / EGR2 and SOX10-mediated initiation of Schwann cell myelination / regulation of nucleotide-excision repair / RSC-type complex / RNA polymerase I preinitiation complex assembly / positive regulation by host of viral transcription / SWI/SNF complex / ATP-dependent chromatin remodeler activity / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear androgen receptor binding / positive regulation of stem cell population maintenance / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of G1/S transition of mitotic cell cycle / negative regulation of cell differentiation / positive regulation of Wnt signaling pathway / positive regulation of myoblast differentiation / ATP-dependent activity, acting on DNA / Chromatin modifying enzymes / DNA polymerase binding / transcription initiation-coupled chromatin remodeling / Interleukin-7 signaling / helicase activity / transcription coregulator binding / positive regulation of cell differentiation / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Formation of the beta-catenin:TCF transactivating complex / lysine-acetylated histone binding / negative regulation of cell growth / kinetochore / fibrillar center / RMTs methylate histone arginines / nuclear matrix / positive regulation of miRNA transcription / transcription corepressor activity / positive regulation of DNA-binding transcription factor activity / p53 binding / nervous system development / positive regulation of cold-induced thermogenesis / transcription coactivator activity / hydrolase activity / chromatin remodeling / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin / nucleolus / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular space / RNA binding / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ ...SWI/SNF complex subunit BRG1 / BRK domain / BRK domain / BRK domain superfamily / domain in transcription and CHROMO domain helicases / domain in helicases and associated with SANT domains / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2, ATP coupling domain / Snf2-ATP coupling, chromatin remodelling complex / Snf2-ATP coupling, chromatin remodelling complex / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Helicase conserved C-terminal domain / Bromodomain-like / Histone Acetyltransferase; Chain A / Bromodomain, conserved site / Bromodomain signature. / helicase superfamily c-terminal domain / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / 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
Transcription activator BRG1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLolli, G. / Caflisch, A.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: High-Throughput Fragment Docking into the BAZ2B Bromodomain: Efficient in Silico Screening for X-Ray Crystallography.
Authors: Lolli, G. / Caflisch, A.
History
DepositionOct 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_ncs_dom_lim
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription activator BRG1
B: Transcription activator BRG1
C: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1939
Polymers46,4843
Non-polymers7096
Water3,819212
1
A: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7313
Polymers15,4951
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7313
Polymers15,4951
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Transcription activator BRG1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7313
Polymers15,4951
Non-polymers2362
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.783, 86.783, 97.959
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
11chain A
21chain B
31chain C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1SERSERGLUGLUchain AAA1452 - 15654 - 117
2LEULEUGLUGLUchain BBB1451 - 15783 - 130
3LEULEUASPASPchain CCC1451 - 15693 - 121

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Components

#1: Protein Transcription activator BRG1 / ATP-dependent helicase SMARCA4 / BRG1-associated factor 190A / BAF190A / Mitotic growth and ...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


Mass: 15494.565 Da / Num. of mol.: 3 / Fragment: Bromodomain, UNP residues 1451-1580
Source method: isolated from a genetically manipulated source
Details: First two residues SM derive from the expression tag
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, BAF190A, BRG1, SNF2B, SNF2L4 / Production host: Escherichia coli (E. coli)
References: UniProt: P51532, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG1000 (12.5%), PEG3350 (12.5%), MPD (12.5%)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.39 Å / Num. obs: 28198 / % possible obs: 99.6 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.05 / Net I/σ(I): 13.1 / Num. measured all: 102791
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2-2.053.70.6782.1751320350.7160.40798
8.94-43.393.80.01464126533210.00899.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.3.11data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4IR5

4ir5


Resolution: 2→43.391 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 1411 5.01 %
Rwork0.1921 26767 -
obs0.1939 28178 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.63 Å2 / Biso mean: 31.6186 Å2 / Biso min: 16 Å2
Refinement stepCycle: final / Resolution: 2→43.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2968 0 40 212 3220
Biso mean--27.65 35.44 -
Num. residues----361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043083
X-RAY DIFFRACTIONf_angle_d0.8654146
X-RAY DIFFRACTIONf_chiral_restr0.035462
X-RAY DIFFRACTIONf_plane_restr0.004526
X-RAY DIFFRACTIONf_dihedral_angle_d14.5041248
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1664X-RAY DIFFRACTION9.576TORSIONAL
12B1664X-RAY DIFFRACTION9.576TORSIONAL
13C1664X-RAY DIFFRACTION9.576TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0002-2.07170.2941400.25212647278798
2.0717-2.15470.27161390.23022648278799
2.1547-2.25270.25661410.21392660280199
2.2527-2.37150.23181400.20782667280799
2.3715-2.52010.23931420.212926782820100
2.5201-2.71460.2521410.213826792820100
2.7146-2.98770.24221410.205126772818100
2.9877-3.41990.23921410.199926782819100
3.4199-4.30810.20081420.160526982840100
4.3081-43.40170.19131440.165227352879100

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