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- PDB-4i6m: Structure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chr... -

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Basic information

Entry
Database: PDB / ID: 4i6m
TitleStructure of Arp7-Arp9-Snf2(HSA)-RTT102 subcomplex of SWI/SNF chromatin remodeler.
Components
  • (Actin-like protein ...) x 2
  • Actin-related protein 7
  • Regulator of Ty1 transposition protein 102
KeywordsTRANSCRIPTION/HYDROLASE / actin-related / chromatin remodeling / TRANSCRIPTION-HYDROLASE complex
Function / homology
Function and homology information


RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation / DNA strand invasion / DNA translocase activity ...RHO GTPases activate IQGAPs / RHO GTPases Activate WASPs and WAVEs / Regulation of actin dynamics for phagocytic cup formation / positive regulation of cell adhesion involved in single-species biofilm formation / positive regulation of mating type switching / positive regulation of invasive growth in response to glucose limitation / aggrephagy / Platelet degranulation / DNA strand invasion / DNA translocase activity / rDNA binding / nucleosome array spacer activity / ATP-dependent chromatin remodeler activity / RSC-type complex / nucleosome disassembly / SWI/SNF complex / nucleosomal DNA binding / NuA4 histone acetyltransferase complex / transcription initiation-coupled chromatin remodeling / histone reader activity / cellular response to amino acid starvation / helicase activity / chromosome segregation / transcription elongation by RNA polymerase II / lysine-acetylated histone binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA-templated DNA replication / heterochromatin formation / double-strand break repair / chromatin organization / RNA polymerase II-specific DNA-binding transcription factor binding / hydrolase activity / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / structural molecule activity / positive regulation of transcription by RNA polymerase II / DNA binding / ATP binding / nucleus
Similarity search - Function
Factor Xa Inhibitor / Factor Xa Inhibitor - #10 / Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / Glutamine-Leucine-Glutamine, QLQ / QLQ / QLQ domain profile. / QLQ / Snf2-ATP coupling, chromatin remodelling complex / Snf2, ATP coupling domain ...Factor Xa Inhibitor / Factor Xa Inhibitor - #10 / Transcription regulator protein Rtt102 / Rtt102p-like transcription regulator protein / 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 / DNA binding domain with preference for A/T rich regions / AT hook, DNA-binding motif / HSA domain / Helicase/SANT-associated domain / HSA domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Other non-globular / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actin / Actin family / Actin / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Special / Helicase conserved C-terminal domain / ATPase, nucleotide binding domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Bromodomain profile. / bromo domain / Bromodomain / Bromodomain-like superfamily / Nucleotidyltransferase; domain 5 / 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 / Alpha-Beta Complex / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Transcription regulatory protein SNF2 / Regulator of Ty1 transposition protein 102 / Actin-like protein ARP9 / Actin-related protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.801 Å
AuthorsSchubert, H.L. / Cairns, B.R. / Hill, C.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structure of an actin-related subcomplex of the SWI/SNF chromatin remodeler.
Authors: Schubert, H.L. / Wittmeyer, J. / Kasten, M.M. / Hinata, K. / Rawling, D.C. / Heroux, A. / Cairns, B.R. / Hill, C.P.
History
DepositionNov 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Source and taxonomy
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Mar 13, 2013Group: Database references
Revision 1.4Aug 16, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Actin-related protein 7
B: Actin-like protein ARP9
C: Actin-like protein ARP9
D: Regulator of Ty1 transposition protein 102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,73016
Polymers135,5914
Non-polymers1,14012
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12850 Å2
ΔGint-125 kcal/mol
Surface area42390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)227.374, 104.138, 81.319
Angle α, β, γ (deg.)90.00, 93.78, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe asymmetric unit contains one biological unit containing four polypeptides, Arp7, Arp9, Snf2(HSA), RTT102.

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Actin-related protein 7 / Actin-like protein ARP7 / Chromatin structure-remodeling complex protein ARP7 / SWI/SNF complex component ARP7


Mass: 54613.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Arp7 and Arp9 are in MSC2 and MSC1 respectively of pRSF.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SNF2, SNF2/YOR290C, SWI2, TYE3, YOR290C, GAM1, HAF1 / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q12406
#4: Protein Regulator of Ty1 transposition protein 102


Mass: 18005.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Snf2 is in MSC1 of pCDF with the full length RTT102 in MSC2.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RTT102, RTT102/YGR275W, YGR275W; / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: P53330

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Actin-like protein ... , 2 types, 2 molecules BC

#2: Protein Actin-like protein ARP9 / Chromatin structure-remodeling complex protein ARP9 / SWI/SNF complex component ARP9


Mass: 50151.816 Da / Num. of mol.: 1 / Fragment: UNP residues 1-246, 275-467
Source method: isolated from a genetically manipulated source
Details: Arp7 and Arp9 are in MSC2 and MSC1 respectively of pRSF.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: ARP9, Arp9/YMR033W, SWP59, YM9973.07, YMR033W / Plasmid: pRSF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q05123
#3: Protein Actin-like protein ARP9 / Chromatin structure-remodeling complex protein ARP9 / SWI/SNF complex component ARP9


Mass: 12820.288 Da / Num. of mol.: 1 / Fragment: HSA domain residues 575-667
Source method: isolated from a genetically manipulated source
Details: Snf2 is in MSC1 of pCDF with the full length RTT102 in MSC2.
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SNF2, SNF2/YOR290C, SWI2, TYE3, YOR290C, GAM1, HAF1 / Plasmid: pCDF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL
References: UniProt: P22082, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Non-polymers , 2 types, 103 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.55 Å3/Da / Density % sol: 65.31 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6 - 2.0 M Ammonium Phosphate, 0.1mM HEPES, pH 7.5, 1mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979, 1.1
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2010 / Details: Si(111)
RadiationMonochromator: Double silicon(111) crystal monochromator with cryogenically-cooled first crystal and sagittally-bent second crystal horizontally-focusing at 3.3:1 demagnification
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.11
ReflectionResolution: 2.8→29.9 Å / Num. obs: 46664 / % possible obs: 98.16 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 77.3 Å2 / Rmerge(I) obs: 0.51 / Net I/σ(I): 18.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.8-2.864.10.03229.44750199.8
4.18-4.784.20.5225.846851100
3.53-3.84.20.8815.646551100
3.02-3.153.90.2994.824631199.9
2.9-3.023.10.3623.044516197.7
2.8-2.92.40.3532.224016186.7

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.801→29.9 Å / SU ML: 0.73 / σ(F): 0 / Phase error: 24.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2226 2287 5 %5%
Rwork0.1845 ---
all0.1865 45768 --
obs0.1865 45768 98.16 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.462 Å2 / ksol: 0.323 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.5688 Å20 Å2-3.3581 Å2
2--11.5406 Å20 Å2
3----6.9718 Å2
Refinement stepCycle: LAST / Resolution: 2.801→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7469 0 60 91 7620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097715
X-RAY DIFFRACTIONf_angle_d1.18110429
X-RAY DIFFRACTIONf_dihedral_angle_d16.7432922
X-RAY DIFFRACTIONf_chiral_restr0.081148
X-RAY DIFFRACTIONf_plane_restr0.0051319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8012-2.86210.41841150.32812205X-RAY DIFFRACTION81
2.8621-2.92860.36821190.3032577X-RAY DIFFRACTION93
2.9286-3.00180.31111460.26862702X-RAY DIFFRACTION98
3.0018-3.08290.30271520.25192730X-RAY DIFFRACTION99
3.0829-3.17350.2651400.22542742X-RAY DIFFRACTION100
3.1735-3.27580.24211560.21692761X-RAY DIFFRACTION100
3.2758-3.39270.27761420.2032780X-RAY DIFFRACTION100
3.3927-3.52830.25311450.18232732X-RAY DIFFRACTION100
3.5283-3.68870.2191350.17332774X-RAY DIFFRACTION100
3.6887-3.88270.18731560.16692760X-RAY DIFFRACTION100
3.8827-4.12540.20341540.15052769X-RAY DIFFRACTION100
4.1254-4.4430.18651570.14032729X-RAY DIFFRACTION100
4.443-4.88840.15771250.13052798X-RAY DIFFRACTION100
4.8884-5.59180.19351550.15442773X-RAY DIFFRACTION100
5.5918-7.030.25151340.20712814X-RAY DIFFRACTION100
7.03-29.96440.2021560.20042835X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 29.8309 Å / Origin y: 35.9826 Å / Origin z: 79.7431 Å
111213212223313233
T0.0567 Å20.0196 Å20.0459 Å2-0.0465 Å20.0357 Å2--0.0328 Å2
L1.2894 °2-0.1104 °2-0.0237 °2-0.7018 °2-0.0394 °2--0.9666 °2
S-0.0162 Å °-0.0834 Å °-0.33 Å °-0.0513 Å °-0.1399 Å °0.3441 Å °0.0218 Å °-0.0907 Å °0.0097 Å °
Refinement TLS groupSelection details: all

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