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- PDB-2y9z: Chromatin Remodeling Factor ISW1a(del_ATPase) in DNA complex -

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Basic information

Entry
Database: PDB / ID: 2y9z
TitleChromatin Remodeling Factor ISW1a(del_ATPase) in DNA complex
Components
  • I-DNA/E-DNA
  • IMITATION SWITCH PROTEIN 1 (DEL_ATPASE)
  • ISWI ONE COMPLEX PROTEIN 3
KeywordsTRANSCRIPTION / NUCLEAR PROTEIN-DNA COMPLEX / CHROMATIN REMODELING / NUCLEOSOME REMODELING
Function / homology
Function and homology information


Isw1b complex / Isw1a complex / negative regulation of histone exchange / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of nucleosome density / : / regulation of chromatin organization / termination of RNA polymerase I transcription / rDNA binding ...Isw1b complex / Isw1a complex / negative regulation of histone exchange / nucleolar chromatin / regulation of transcriptional start site selection at RNA polymerase II promoter / regulation of nucleosome density / : / regulation of chromatin organization / termination of RNA polymerase I transcription / rDNA binding / DNA-templated transcription, elongation / nucleosome positioning / nucleosome binding / ATP-dependent chromatin remodeler activity => GO:0140658 / sister chromatid cohesion / termination of RNA polymerase II transcription / chromatin remodeling => GO:0006338 / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / ATP-dependent activity, acting on DNA / helicase activity / chromatin remodeling / transcription cis-regulatory region binding / hydrolase activity / positive regulation of transcription by RNA polymerase II / ATP binding / nucleus
Similarity search - Function
ISWI, HAND domain / iswi atpase / Isw1/2, N-terminal / SLIDE / HAND / ISWI, HAND domain superfamily / SLIDE domain / ISWI, HAND domain / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 ...ISWI, HAND domain / iswi atpase / Isw1/2, N-terminal / SLIDE / HAND / ISWI, HAND domain superfamily / SLIDE domain / ISWI, HAND domain / WHIM1 domain / WSTF, HB1, Itc1p, MBD9 motif 1 / SANT domain profile. / SANT domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / SNF2-like, N-terminal domain superfamily / SNF2-related domain / SNF2, N-terminal / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeodomain-like / Helicase conserved C-terminal domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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. / Helicase, C-terminal / DEAD-like helicases superfamily / 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
DNA (> 10) / DNA / ISWI chromatin-remodeling complex ATPase ISW1 / ISWI one complex protein 3
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (baker's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.601 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 / Version format compliance
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
C: I-DNA/E-DNA
D: I-DNA/E-DNA
E: I-DNA/E-DNA
F: I-DNA/E-DNA


Theoretical massNumber of molelcules
Total (without water)175,8886
Polymers175,8886
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12791 Å2
ΔGint-60.4 kcal/mol
Surface area65973 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)284.028, 284.028, 193.423
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 44327.895 Da / Num. of mol.: 1 / Fragment: HAND, SANT, SLIDE DOMAINS, RESIDUES 763-1129
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker'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: 72422.539 Da / Num. of mol.: 1
Fragment: CORE DOMAIN CONTAINING CLB AND HLB SUBDOMAINS, RESIDUES 127-749
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (baker's yeast)
Plasmid: MULTIBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF21 / References: UniProt: P43596
#3: DNA chain
I-DNA/E-DNA


Mass: 14784.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: 48 BASES, C-D I-DNA DUPLEX, E-F E-DNA DUPLEX / Source: (synth.) SACCHAROMYCES CEREVISIAE (baker's yeast)

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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: 6.7 Å3/Da / Density % sol: 83 % / Description: NONE
Crystal growpH: 7
Details: 50MM BISTRIS(PH7.0), 150MM NACITRATE, 30%(W/V) PEG5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 18, 2009
RadiationMonochromator: LN2 COOLED FIXED-EXIT SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.6→30 Å / Num. obs: 53279 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 118.01 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.9
Reflection shellResolution: 3.6→3.67 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2 / % possible all: 99.8

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Processing

Software
NameClassification
XDSdata reduction
SCALAdata scaling
HKL2MAPphasing
SHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 3.601→29.955 Å / SU ML: 0.47 / σ(F): 1.32 / Phase error: 32.1 / Stereochemistry target values: MLHL
Details: CHAIN A RESIDUES N-TERMINUS TO 788 ARE DISORDERED. CHAIN A RESIDUES 1076 TO C-TERMINUS ARE DISORDERED. CHAIN B RESIDUES N-TERMINUS TO 133 ARE DISORDERED. CHAIN B RESIDUES 658 TO 677 ARE ...Details: CHAIN A RESIDUES N-TERMINUS TO 788 ARE DISORDERED. CHAIN A RESIDUES 1076 TO C-TERMINUS ARE DISORDERED. CHAIN B RESIDUES N-TERMINUS TO 133 ARE DISORDERED. CHAIN B RESIDUES 658 TO 677 ARE DISORDERED. CHAIN B RESIDUES 749 TO C-TERMINUS ARE DISORDERED. CHAIN C BASES 1 TO 7 ARE DISORDERED. CHAIN C BASES 39 TO 48 ARE DISORDERED. CHAIN D BASES 1 TO 10 ARE DISORDERED. CHAIN D BASES 42 TO 48 ARE DISORDERED. CHAIN E BASES 1 TO 24 ARE DISORDERED. CHAIN E BASE 48 IS DISORDERED. CHAIN F BASE 1 IS DISORDERED. CHAIN F BASES 25 TO 48 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.2914 2656 5 %
Rwork0.2829 --
obs0.2833 53279 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 95.002 Å2 / ksol: 0.313 e/Å3
Displacement parametersBiso mean: 172.3 Å2
Baniso -1Baniso -2Baniso -3
1--16.214 Å2-0 Å20 Å2
2---16.214 Å2-0 Å2
3---25.4131 Å2
Refinement stepCycle: LAST / Resolution: 3.601→29.955 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7286 2214 0 0 9500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110127
X-RAY DIFFRACTIONf_angle_d0.70313884
X-RAY DIFFRACTIONf_dihedral_angle_d18.9413922
X-RAY DIFFRACTIONf_chiral_restr0.0431499
X-RAY DIFFRACTIONf_plane_restr0.0041412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6014-3.66680.38321490.38022569X-RAY DIFFRACTION98
3.6668-3.73720.40561650.3812593X-RAY DIFFRACTION100
3.7372-3.81330.37841350.37522619X-RAY DIFFRACTION100
3.8133-3.89610.37751330.38552624X-RAY DIFFRACTION100
3.8961-3.98650.38321320.37232628X-RAY DIFFRACTION100
3.9865-4.08590.41071300.36932643X-RAY DIFFRACTION100
4.0859-4.19610.35181330.36532658X-RAY DIFFRACTION100
4.1961-4.31930.37211290.35082624X-RAY DIFFRACTION100
4.3193-4.45820.32731330.33552662X-RAY DIFFRACTION100
4.4582-4.6170.34091540.29212625X-RAY DIFFRACTION100
4.617-4.80120.2931330.29872662X-RAY DIFFRACTION100
4.8012-5.01870.26811300.27342649X-RAY DIFFRACTION100
5.0187-5.2820.29471520.27042670X-RAY DIFFRACTION100
5.282-5.61090.28161390.26932662X-RAY DIFFRACTION100
5.6109-6.04080.27951420.25622687X-RAY DIFFRACTION100
6.0408-6.64270.27361580.2462672X-RAY DIFFRACTION100
6.6427-7.59030.22471190.22232738X-RAY DIFFRACTION100
7.5903-9.51180.21071400.18692757X-RAY DIFFRACTION100
9.5118-29.95570.19731500.21852881X-RAY DIFFRACTION100
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.39962.1566-0.28714.9384-1.1269-0.51320.0419-0.0393-0.3127-0.5512-0.0006-0.6280.1823-0.20310.01881.4218-0.07430.15140.50770.09630.7325108.1888-16.910570.6277
22.1926-0.6281-0.29692.74570.43571.9071-0.1720.1545-0.0913-0.20940.13670.03170.0151-0.22910.0670.4230.06840.09460.01340.04540.1047111.026536.341163.2633
30.82390.34770.91981.326-0.07710.6731-0.04410.2797-0.1817-0.5847-0.1520.03510.50710.24580.10342.9965-0.4893-0.01652.66290.08372.54693.9676-4.085859.7705
42.76710.98541.88531.6885-0.81281.80270.5118-0.7776-0.1220.22080.4030.07650.1505-0.1344-0.6051.03180.01680.06211.0557-0.28510.8746155.113745.434381.4672
51.26591.4609-0.30212.359-0.9617-0.1593-0.1026-0.84250.2650.8747-0.51980.00850.4544-0.00470.47381.16230.2541-0.0870.9275-0.26740.7189156.240246.585881.7018
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN E
5X-RAY DIFFRACTION5CHAIN F

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