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- PDB-2y9y: Chromatin Remodeling Factor ISW1a(del_ATPase) -

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Basic information

Entry
Database: PDB / ID: 2y9y
TitleChromatin Remodeling Factor ISW1a(del_ATPase)
Components
  • IMITATION SWITCH PROTEIN 1 (DEL_ATPASE)
  • ISWI ONE COMPLEX PROTEIN 3
KeywordsTRANSCRIPTION / NUCLEAR PROTEIN COMPLEX / CHROMATIN REMODELING / NUCLEOSOME REMODELING
Function / homology
Function and homology information


Isw1b complex / Isw1a complex / Isw1 complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of RNA export from nucleus / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding ...Isw1b complex / Isw1a complex / Isw1 complex / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / negative regulation of RNA export from nucleus / negative regulation of IRE1-mediated unfolded protein response / DNA-templated transcription elongation / regulation of chromatin organization / rDNA binding / nucleosome array spacer activity / sister chromatid cohesion / termination of RNA polymerase II transcription / termination of RNA polymerase I transcription / nucleosome binding / helicase activity / mRNA 3'-UTR binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / heterochromatin formation / response to heat / hydrolase activity / transcription cis-regulatory region binding / chromatin remodeling / chromatin binding / regulation of DNA-templated transcription / chromatin / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus
Similarity search - Function
ISWI, HAND domain / iswi atpase / Isw1/2, N-terminal / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE ...ISWI, HAND domain / iswi atpase / Isw1/2, N-terminal / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / ISWI, HAND domain / SLIDE domain / ISWI, HAND domain superfamily / HAND / SLIDE / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / SANT domain profile. / SANT domain / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helicase conserved C-terminal domain / Homeobox-like domain 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 / Arc Repressor Mutant, subunit A / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ISWI chromatin-remodeling complex ATPase ISW1 / ISWI one complex protein 3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.25 Å
AuthorsYamada, K. / Frouws, T.D. / Angst, B. / Fitzgerald, D.J. / DeLuca, C. / Schimmele, K. / Sargent, D.F. / Richmond, T.J.
CitationJournal: Nature / Year: 2011
Title: Structure and mechanism of the chromatin remodelling factor ISW1a.
Authors: Kazuhiro Yamada / Timothy D Frouws / Brigitte Angst / Daniel J Fitzgerald / Carl DeLuca / Kyoko Schimmele / David F Sargent / Timothy J Richmond /
Abstract: Site-specific recognition of DNA in eukaryotic organisms depends on the arrangement of nucleosomes in chromatin. In the yeast Saccharomyces cerevisiae, ISW1a and related chromatin remodelling factors ...Site-specific recognition of DNA in eukaryotic organisms depends on the arrangement of nucleosomes in chromatin. In the yeast Saccharomyces cerevisiae, ISW1a and related chromatin remodelling factors are implicated in establishing the nucleosome repeat during replication and altering nucleosome position to affect gene activity. Here we have solved the crystal structures of S. cerevisiae ISW1a lacking its ATPase domain both alone and with DNA bound at resolutions of 3.25 Å and 3.60 Å, respectively, and we have visualized two different nucleosome-containing remodelling complexes using cryo-electron microscopy. The composite X-ray and electron microscopy structures combined with site-directed photocrosslinking analyses of these complexes suggest that ISW1a uses a dinucleosome substrate for chromatin remodelling. Results from a remodelling assay corroborate the dinucleosome model. We show how a chromatin remodelling factor could set the spacing between two adjacent nucleosomes acting as a 'protein ruler'.
History
DepositionFeb 17, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references / Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IMITATION SWITCH PROTEIN 1 (DEL_ATPASE)
B: ISWI ONE COMPLEX PROTEIN 3


Theoretical massNumber of molelcules
Total (without water)116,7782
Polymers116,7782
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-16 kcal/mol
Surface area48020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)206.971, 206.971, 215.308
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein IMITATION SWITCH PROTEIN 1 (DEL_ATPASE) / ISWI CHROMATIN-REMODELING COMPLEX ATPASE ISW1 / ISW1


Mass: 44339.883 Da / Num. of mol.: 1 / Fragment: HAND, SANT, SLIDE DOMAINS, RESIDUES 763-1129 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: MULTIBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: P38144
#2: Protein ISWI ONE COMPLEX PROTEIN 3 / IOC3


Mass: 72437.617 Da / Num. of mol.: 1
Fragment: CORE DOMAIN CONTAINING CLB AND HLB SUBDOMAINS, RESIDUES 127-749
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: MULTIBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: P43596
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 815 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASP 844 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, LYS 815 TO GLN ENGINEERED RESIDUE IN CHAIN A, ASP 844 TO LYS ENGINEERED RESIDUE IN CHAIN A, GLU 848 TO GLN ENGINEERED RESIDUE IN CHAIN A, LYS 851 TO GLN ENGINEERED RESIDUE IN CHAIN A, GLN 853 TO GLU ENGINEERED RESIDUE IN CHAIN B, ASN 682 TO LYS

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 8

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68 % / Description: NONE
Crystal growpH: 6.5
Details: 100MM BISTRIS, PH 7.0, 1.6M NA-CITRATE, 10% GLYCEROL, 0.1M NA PHOSPHATE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2008
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→30 Å / Num. obs: 28004 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.9 % / Biso Wilson estimate: 119.96 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 3.6
Reflection shellResolution: 3.25→3.36 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.2 / % possible all: 100

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Processing

Software
NameClassification
XDSdata reduction
SCALAdata scaling
SHARPphasing
SOLOMONphasing
PHENIXrefinement
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 3.25→29.874 Å / SU ML: 0.45 / σ(F): 1.62 / Phase error: 31.73 / Stereochemistry target values: MLHL
Details: CHAIN A RESIDUES N-TERMINUS TO 790 ARE DISORDERED. CHAIN A RESIDUES 1068 TO C-TERMINUS ARE DISORDERED. CHAIN B RESIDUES N-TERMINUS TO 137 ARE DISORDERED. CHAIN B RESIDUES 662 TO 678 ARE ...Details: CHAIN A RESIDUES N-TERMINUS TO 790 ARE DISORDERED. CHAIN A RESIDUES 1068 TO C-TERMINUS ARE DISORDERED. CHAIN B RESIDUES N-TERMINUS TO 137 ARE DISORDERED. CHAIN B RESIDUES 662 TO 678 ARE DISORDERED. CHAIN B RESIDUES 747 TO C-TERMINUS ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2965 1416 5.1 %
Rwork0.2832 --
obs0.2838 28004 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 99 Å2 / ksol: 0.308 e/Å3
Displacement parametersBiso mean: 153.9 Å2
Baniso -1Baniso -2Baniso -3
1-8.2764 Å20 Å20 Å2
2--8.2764 Å20 Å2
3----16.5529 Å2
Refinement stepCycle: LAST / Resolution: 3.25→29.874 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7170 0 0 0 7170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027343
X-RAY DIFFRACTIONf_angle_d0.4679911
X-RAY DIFFRACTIONf_dihedral_angle_d10.6052807
X-RAY DIFFRACTIONf_chiral_restr0.0321052
X-RAY DIFFRACTIONf_plane_restr0.0021284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.3660.40281370.37872633X-RAY DIFFRACTION100
3.366-3.50060.40551430.36652639X-RAY DIFFRACTION100
3.5006-3.65970.31241370.34462631X-RAY DIFFRACTION100
3.6597-3.85220.33741410.33452629X-RAY DIFFRACTION100
3.8522-4.0930.33081520.31592657X-RAY DIFFRACTION100
4.093-4.40810.29761320.28872631X-RAY DIFFRACTION100
4.4081-4.850.27821390.27052657X-RAY DIFFRACTION100
4.85-5.5480.29811500.27122670X-RAY DIFFRACTION100
5.548-6.97510.28361430.27112681X-RAY DIFFRACTION100
6.9751-29.87490.24581420.23022760X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.74860.70570.92782.87150.10481.02460.0631-1.10750.15120.2876-0.03520.64920.18060.07950.16360.85530.01770.18040.9925-0.43881.457384.21159.47591.8572
25.176-2.6079-1.0333.27913.38064.45750.13920.7604-0.78510.69080.0897-0.67441.13450.1631-0.33841.17240.1865-0.14491.0838-0.47181.844356.677913.222715.5053
39.66690.6095-3.92640.0693-0.07712.3124-0.76550.4109-2.3998-0.2454-0.13690.00550.8707-0.02060.84031.54710.158-0.21110.9438-0.31031.559846.92936.763431.9988
41.21040.54960.46433.85052.82022.29650.30540.0844-0.55241.1063-0.4208-0.11270.5023-0.22120.1170.9245-0.2086-0.03940.6377-0.05541.355436.222714.863945.5333
52.49310.15650.03121.2564-0.94743.72730.1336-0.11420.08320.1647-0.12530.39940.2855-0.51250.01430.6218-0.1502-0.13620.3717-0.15730.504730.633940.051858.6555
61.9333-3.6714-2.09426.79133.92972.2319-0.27890.5528-0.8873-0.30250.0148-0.04470.7262-0.00120.19770.9928-0.13530.02580.734-0.42690.963636.635723.494725.0481
74.54871.53850.3541.64532.19353.85130.1392-0.7256-1.13440.4982-0.4403-0.09760.7093-0.1225-1.22120.2324-0.1096-0.24690.308-0.2178-0.200735.971733.745456.1188
83.303-1.91980.66072.5846-2.41223.1489-0.5926-0.4642-0.15440.3415-0.022-0.02730.71060.12280.40822.15380.0003-0.32711.6210.34381.556133.111410.050991.018
90.7027-0.5-0.44961.44440.73551.13860.0804-0.309-0.4770.712-0.15790.19260.1389-0.217-0.22871.0979-0.23610.12671.03880.01410.935718.243634.076370.6788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 791:886
2X-RAY DIFFRACTION2CHAIN A AND RESID 887:939
3X-RAY DIFFRACTION3CHAIN A AND RESID 940:970
4X-RAY DIFFRACTION4CHAIN A AND RESID 971:1067
5X-RAY DIFFRACTION5CHAIN B AND RESID 138:314
6X-RAY DIFFRACTION6CHAIN B AND RESID 315:368
7X-RAY DIFFRACTION7CHAIN B AND RESID 369:436
8X-RAY DIFFRACTION8CHAIN B AND RESID 437:522
9X-RAY DIFFRACTION9CHAIN B AND RESID 523:746

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