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- PDB-7vrb: Structure of the Human BRG1/SS18 complex -

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Basic information

Entry
Database: PDB / ID: 7vrb
TitleStructure of the Human BRG1/SS18 complex
ComponentsSMARCA4 protein,Protein SSXT
KeywordsONCOPROTEIN / four-helix bundle
Function / homology
Function and homology information


npBAF complex / neuronal stem cell population maintenance / SWI/SNF complex / ephrin receptor signaling pathway / nuclear receptor coactivator activity / helicase activity / cell morphogenesis / microtubule cytoskeleton organization / microtubule cytoskeleton / chromatin organization ...npBAF complex / neuronal stem cell population maintenance / SWI/SNF complex / ephrin receptor signaling pathway / nuclear receptor coactivator activity / helicase activity / cell morphogenesis / microtubule cytoskeleton organization / microtubule cytoskeleton / chromatin organization / histone binding / intracellular signal transduction / response to xenobiotic stimulus / regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus
Similarity search - Function
SS18, N-terminal / SS18 family / SSXT protein (N-terminal region) / 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 ...SS18, N-terminal / SS18 family / SSXT protein (N-terminal region) / 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, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
SMARCA4 protein / Protein SSXT
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.389 Å
AuthorsCheng, Y. / Chen, F. / Zhou, H. / Long, J.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870750 China
National Natural Science Foundation of China (NSFC)31670758 China
CitationJournal: Nat Commun / Year: 2022
Title: Phase transition and remodeling complex assembly are important for SS18-SSX oncogenic activity in synovial sarcomas.
Authors: Cheng, Y. / Shen, Z. / Gao, Y. / Chen, F. / Xu, H. / Mo, Q. / Chu, X. / Peng, C.L. / McKenzie, T.T. / Palacios, B.E. / Hu, J. / Zhou, H. / Long, J.
History
DepositionOct 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 25, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SMARCA4 protein,Protein SSXT
B: SMARCA4 protein,Protein SSXT
C: SMARCA4 protein,Protein SSXT
D: SMARCA4 protein,Protein SSXT


Theoretical massNumber of molelcules
Total (without water)62,7594
Polymers62,7594
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, immunoprecipitation, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-45 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.607, 105.829, 225.857
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11B-52-

GLN

21D-219-

HOH

31D-235-

HOH

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Components

#1: Protein
SMARCA4 protein,Protein SSXT / / Protein SYT / Synovial sarcoma translocated to X chromosome protein


Mass: 15689.859 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: BRG1-SS18,BRG1-SS18 / Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCA4, SS18, SSXT, SYT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B9EGQ8, UniProt: Q15532
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.42 Å3/Da / Density % sol: 49.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.16 M sodium phosphate monobasic monohydrate and 0.24 M potassium phosphate dibasic

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9788 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.389→28.232 Å / Num. obs: 24275 / % possible obs: 99.9 % / Redundancy: 13.1 % / Rpim(I) all: 0.018 / Net I/σ(I): 39.16
Reflection shellResolution: 2.39→2.43 Å / Num. unique obs: 1205 / Rpim(I) all: 0.297

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.389→28.232 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 1274 5.29 %
Rwork0.2045 22810 -
obs0.207 24084 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.55 Å2 / Biso mean: 43.6616 Å2 / Biso min: 14.51 Å2
Refinement stepCycle: final / Resolution: 2.389→28.232 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3393 0 0 154 3547
Biso mean---42.98 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083446
X-RAY DIFFRACTIONf_angle_d0.8854646
X-RAY DIFFRACTIONf_chiral_restr0.045511
X-RAY DIFFRACTIONf_plane_restr0.006620
X-RAY DIFFRACTIONf_dihedral_angle_d15.6022152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.389-2.48460.33681100.2535239994
2.4846-2.59760.30631520.23642518100
2.5976-2.73450.2891310.24582535100
2.7345-2.90560.29581430.23252543100
2.9056-3.12970.30151550.22142516100
3.1297-3.44420.25121240.20632571100
3.4442-3.94140.21431250.18242574100
3.9414-4.96140.20981650.17642565100
4.9614-6.480.23541690.1962258998

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