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- PDB-5ikf: Crystal structure of the C-terminal domain of the Mit1 nucleosome... -

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Basic information

Entry
Database: PDB / ID: 5ikf
TitleCrystal structure of the C-terminal domain of the Mit1 nucleosome remodeler in complex with Clr1
Components
  • Chromatin remodeling factor mit1
  • Cryptic loci regulator protein 1
KeywordsTRANSCRIPTION / zinc fingers / alpha-helical / protein-protein interface / complex
Function / homology
Function and homology information


SHREC complex / : / mating-type region heterochromatin / heterochromatin island / chromosome, subtelomeric region / rDNA heterochromatin / nucleosome organization / ATP-dependent chromatin remodeler activity / silent mating-type cassette heterochromatin formation / pericentric heterochromatin ...SHREC complex / : / mating-type region heterochromatin / heterochromatin island / chromosome, subtelomeric region / rDNA heterochromatin / nucleosome organization / ATP-dependent chromatin remodeler activity / silent mating-type cassette heterochromatin formation / pericentric heterochromatin / nucleosome binding / heterochromatin formation / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / chromatin organization / histone binding / chromatin remodeling / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / nucleus
Similarity search - Function
Mit1, C-terminal Zn finger 2 / Chromatin remodeling factor Mit1, C-terminal Zn finger 1 / Chromatin remodeling factor Mit1 C-terminal Zn finger 2 / Chromatin remodeling factor Mit1 C-terminal Zn finger 1 / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / zinc finger / Zinc finger C2H2 type domain profile. ...Mit1, C-terminal Zn finger 2 / Chromatin remodeling factor Mit1, C-terminal Zn finger 1 / Chromatin remodeling factor Mit1 C-terminal Zn finger 2 / Chromatin remodeling factor Mit1 C-terminal Zn finger 1 / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helicase conserved C-terminal domain / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / 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 / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Cryptic loci regulator protein 1 / Chromatin remodeling factor mit1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsBrugger, C. / Schalch, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_139137-1 Switzerland
CitationJournal: Mol.Cell / Year: 2016
Title: SHREC Silences Heterochromatin via Distinct Remodeling and Deacetylation Modules.
Authors: Job, G. / Brugger, C. / Xu, T. / Lowe, B.R. / Pfister, Y. / Qu, C. / Shanker, S. / Banos Sanz, J.I. / Partridge, J.F. / Schalch, T.
History
DepositionMar 3, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Chromatin remodeling factor mit1
B: Cryptic loci regulator protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2156
Polymers47,0132
Non-polymers2024
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-67 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.680, 52.850, 81.970
Angle α, β, γ (deg.)90.00, 115.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Chromatin remodeling factor mit1 / Mi2-like interacting with clr3 protein 1 / Snf2/Hdac-containing repressor complex protein mit1 / ...Mi2-like interacting with clr3 protein 1 / Snf2/Hdac-containing repressor complex protein mit1 / SHREC protein mit1


Mass: 29457.162 Da / Num. of mol.: 1 / Fragment: UNP residues 1156-1417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: mit1, SPBP35G2.10 / Plasmid: p5395 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9P793, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Protein Cryptic loci regulator protein 1


Mass: 17556.061 Da / Num. of mol.: 1 / Fragment: UNP residues 357-500
Source method: isolated from a genetically manipulated source
Details: T7 tagged fragment of Clr1 containing residues 353-500
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: clr1, SPBC2D10.17 / Plasmid: p5394 / Details (production host): pAceBac1xpIDK Multibac / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O74808
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.19 Å3/Da / Density % sol: 43.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Sodium bromide, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.8→47.64 Å / Num. obs: 10218 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 56 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.059 / Net I/σ(I): 21
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 4.5 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152: ???)refinement
XDSdata reduction
Aimlessdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→46.217 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.28 / Phase error: 27.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1983 10.09 %
Rwork0.1994 --
obs0.2041 10217 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→46.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 0 4 30 2305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032321
X-RAY DIFFRACTIONf_angle_d0.4493118
X-RAY DIFFRACTIONf_dihedral_angle_d11.7461450
X-RAY DIFFRACTIONf_chiral_restr0.036356
X-RAY DIFFRACTIONf_plane_restr0.003400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.30361440.29551279X-RAY DIFFRACTION100
2.87-2.94760.27751420.28891267X-RAY DIFFRACTION100
2.9476-3.03430.30821390.25351232X-RAY DIFFRACTION100
3.0343-3.13230.32281390.23771252X-RAY DIFFRACTION100
3.1323-3.24420.29381400.24171283X-RAY DIFFRACTION100
3.2442-3.3740.2971360.24111260X-RAY DIFFRACTION100
3.374-3.52750.30071380.23291268X-RAY DIFFRACTION100
3.5275-3.71340.23291440.19721273X-RAY DIFFRACTION100
3.7134-3.9460.2171450.18081260X-RAY DIFFRACTION100
3.946-4.25050.21861410.16341263X-RAY DIFFRACTION100
4.2505-4.67780.18881390.17041229X-RAY DIFFRACTION100
4.6778-5.35390.25191500.17821300X-RAY DIFFRACTION100
5.3539-6.7420.23871460.19451251X-RAY DIFFRACTION100
6.742-46.22320.22141400.17541256X-RAY DIFFRACTION100

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