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- PDB-7cyu: Crystal structure of human BAF57 HMG domain -

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Basic information

Entry
Database: PDB / ID: 7cyu
TitleCrystal structure of human BAF57 HMG domain
ComponentsSWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
KeywordsDNA BINDING PROTEIN / Chromatin remodeling / SWI/SNF
Function / homology
Function and homology information


bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of G0 to G1 transition / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / N-acetyltransferase activity / SWI/SNF complex ...bBAF complex / npBAF complex / brahma complex / nBAF complex / regulation of G0 to G1 transition / nucleosome disassembly / regulation of nucleotide-excision repair / RSC-type complex / N-acetyltransferase activity / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of T cell differentiation / nuclear chromosome / 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 / positive regulation of myoblast differentiation / neurogenesis / nuclear receptor binding / positive regulation of cell differentiation / kinetochore / RMTs methylate histone arginines / nuclear matrix / transcription coactivator activity / chromatin remodeling / negative regulation of DNA-templated transcription / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / nucleoplasm / nucleus
Similarity search - Function
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
Similarity search - Domain/homology
SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsHeo, Y. / Yun, J.H. / Park, J.H. / Lee, W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of the HMG domain of human BAF57 and its interaction with four-way junction DNA.
Authors: Heo, Y. / Park, J.H. / Kim, J. / Han, J. / Yun, J.H. / Lee, W.
History
DepositionSep 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7483
Polymers8,5561
Non-polymers1922
Water28816
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-13 kcal/mol
Surface area5040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.873, 58.873, 50.263
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-306-

HOH

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Components

#1: Protein SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1 / BRG1-associated factor 57 / BAF57


Mass: 8555.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCE1, BAF57 / Production host: Escherichia coli (E. coli) / References: UniProt: Q969G3
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.94 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 2.0M Ammonium sulfate, 0.1M Sodium acetate

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 3481 / % possible obs: 98.9 % / Redundancy: 7 % / Biso Wilson estimate: 55.97 Å2 / CC1/2: 0.998 / Net I/σ(I): 21.62
Reflection shellResolution: 2.55→2.59 Å / Mean I/σ(I) obs: 1.88 / Num. unique obs: 312 / CC1/2: 0.844 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tq6
Resolution: 2.55→35.79 Å / SU ML: 0.3541 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 29.7831 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2748 352 10.11 %
Rwork0.2334 3129 -
obs0.2377 3481 99.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.54 Å2
Refinement stepCycle: LAST / Resolution: 2.55→35.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms531 0 10 16 557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026552
X-RAY DIFFRACTIONf_angle_d0.4713744
X-RAY DIFFRACTIONf_chiral_restr0.033171
X-RAY DIFFRACTIONf_plane_restr0.004193
X-RAY DIFFRACTIONf_dihedral_angle_d10.1234332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.920.31761120.26821009X-RAY DIFFRACTION98.68
2.92-3.670.30061170.26231042X-RAY DIFFRACTION100
3.67-35.790.25561230.21351078X-RAY DIFFRACTION100

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