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- PDB-6yxp: Higher resolution structure of the N-terminal module of the human... -

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Basic information

Entry
Database: PDB / ID: 6yxp
TitleHigher resolution structure of the N-terminal module of the human SWI/SNF-subunit BAF155/SMARCC1
ComponentsSWI/SNF complex subunit SMARCC1
KeywordsSIGNALING PROTEIN / Baf155 / SWI/SNF-subunit
Function / homology
Function and homology information


prostate gland development / npBAF complex / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / nucleosome disassembly / regulation of nucleotide-excision repair / XY body / RSC-type complex ...prostate gland development / npBAF complex / brahma complex / nBAF complex / GBAF complex / regulation of G0 to G1 transition / nucleosome disassembly / regulation of nucleotide-excision repair / XY body / RSC-type complex / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of T cell differentiation / 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 / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of myoblast differentiation / nucleosomal DNA binding / male germ cell nucleus / positive regulation of cell differentiation / animal organ morphogenesis / kinetochore / RMTs methylate histone arginines / nuclear matrix / insulin receptor signaling pathway / nervous system development / histone binding / transcription coactivator activity / chromatin remodeling / positive regulation of cell population proliferation / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / SMARCC, C-terminal / SWIRM-associated region 1 / SWIRM domain / SWIRM domain ...SMARCC, SWIRM-associated domain / SMARCC, N-terminal / : / SWIRM-associated domain at the N-terminal / SWIRM-associated domain at the C-terminal / MarR-like, BRCT and chromo domains module profile. / SMARCC, C-terminal / SWIRM-associated region 1 / SWIRM domain / SWIRM domain / SWIRM domain profile. / SANT domain profile. / SANT domain / Chromo/chromo shadow domain / Chromatin organization modifier domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / BRCT domain superfamily / Homeobox-like domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
SWI/SNF complex subunit SMARCC1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAllen, M.D. / Bycroft, M. / Zinzalla, G.
CitationJournal: Commun Biol / Year: 2021
Title: SWI/SNF subunit BAF155 N-terminus structure informs the impact of cancer-associated mutations and reveals a potential drug binding site.
Authors: Allen, M.D. / Freund, S.M.V. / Bycroft, M. / Zinzalla, G.
History
DepositionMay 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SWI/SNF complex subunit SMARCC1
B: SWI/SNF complex subunit SMARCC1


Theoretical massNumber of molelcules
Total (without water)65,7082
Polymers65,7082
Non-polymers00
Water9,278515
1
A: SWI/SNF complex subunit SMARCC1


Theoretical massNumber of molelcules
Total (without water)32,8541
Polymers32,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SWI/SNF complex subunit SMARCC1


Theoretical massNumber of molelcules
Total (without water)32,8541
Polymers32,8541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.900, 138.322, 56.510
Angle α, β, γ (deg.)90.00, 110.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SWI/SNF complex subunit SMARCC1 / BRG1-associated factor 155 / BAF155 / SWI/SNF complex 155 kDa subunit / SWI/SNF-related matrix- ...BRG1-associated factor 155 / BAF155 / SWI/SNF complex 155 kDa subunit / SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily C member 1


Mass: 32854.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMARCC1, BAF155 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q92922
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.45 Å3/Da / Density % sol: 49.77 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.2 M Magnesium formate (pH 5.9), 20% PEG 3350. Protein at 16 mg/ml.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.939273 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939273 Å / Relative weight: 1
ReflectionResolution: 1.6→49.49 Å / Num. obs: 82320 / % possible obs: 99.1 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Net I/σ(I): 15.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 11930 / CC1/2: 0.85 / Rpim(I) all: 0.248 / Rrim(I) all: 0.661 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YXO

6yxo


Resolution: 1.6→42.066 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.1
RfactorNum. reflection% reflection
Rfree0.1978 4073 4.95 %
Rwork0.1727 --
obs0.174 82266 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→42.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4509 0 0 515 5024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064639
X-RAY DIFFRACTIONf_angle_d0.86285
X-RAY DIFFRACTIONf_dihedral_angle_d2.8582777
X-RAY DIFFRACTIONf_chiral_restr0.055651
X-RAY DIFFRACTIONf_plane_restr0.005807
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.61880.36661540.2772561X-RAY DIFFRACTION93
1.6188-1.63860.30631590.26772608X-RAY DIFFRACTION99
1.6386-1.65930.30591410.25482758X-RAY DIFFRACTION100
1.6593-1.68110.27261190.2392714X-RAY DIFFRACTION100
1.6811-1.70420.27061540.22732699X-RAY DIFFRACTION100
1.7042-1.72850.28431250.21722686X-RAY DIFFRACTION100
1.7285-1.75430.2341490.21282750X-RAY DIFFRACTION100
1.7543-1.78170.22371210.20332670X-RAY DIFFRACTION100
1.7817-1.81090.25341370.19862731X-RAY DIFFRACTION100
1.8109-1.84220.24031450.1982713X-RAY DIFFRACTION100
1.8422-1.87570.19761490.19612699X-RAY DIFFRACTION99
1.8757-1.91170.21121190.19282690X-RAY DIFFRACTION99
1.9117-1.95080.21061430.20442686X-RAY DIFFRACTION98
1.9508-1.99320.21911460.19762687X-RAY DIFFRACTION98
1.9932-2.03960.2381200.19652683X-RAY DIFFRACTION100
2.0396-2.09060.20111260.19432767X-RAY DIFFRACTION100
2.0906-2.14710.22491480.18352673X-RAY DIFFRACTION100
2.1471-2.21030.21461450.18972703X-RAY DIFFRACTION99
2.2103-2.28160.19981460.18012693X-RAY DIFFRACTION100
2.2816-2.36310.22711310.18612726X-RAY DIFFRACTION100
2.3631-2.45770.19161490.18932724X-RAY DIFFRACTION100
2.4577-2.56960.21271540.18122678X-RAY DIFFRACTION99
2.5696-2.7050.21551730.18062661X-RAY DIFFRACTION99
2.705-2.87450.20361380.1882725X-RAY DIFFRACTION100
2.8745-3.09630.20481220.17652711X-RAY DIFFRACTION99
3.0963-3.40780.18551520.17352692X-RAY DIFFRACTION99
3.4078-3.90060.18141510.15462581X-RAY DIFFRACTION95
3.9006-4.91320.16851240.13522757X-RAY DIFFRACTION100
4.9132-42.0660.15891330.14432767X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.2151 Å / Origin y: 50.3313 Å / Origin z: 67.6816 Å
111213212223313233
T0.1576 Å2-0.0099 Å20.0031 Å2-0.179 Å2-0.0051 Å2--0.1483 Å2
L0.2652 °2-0.081 °20.075 °2-0.7066 °20.1969 °2--0.4255 °2
S0.0231 Å °0.0024 Å °-0.0248 Å °0.0807 Å °-0.027 Å °-0.0272 Å °-0.0548 Å °-0.0087 Å °-0.0001 Å °
Refinement TLS groupSelection details: all

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