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- PDB-6fto: Crystal structure of the Chp2 chromoshadow domain in complex with... -

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Basic information

Entry
Database: PDB / ID: 6fto
TitleCrystal structure of the Chp2 chromoshadow domain in complex with N-terminal domain of chromatin remodeler Mit1
Components
  • Chromatin remodeling factor mit1
  • Chromo domain-containing protein 2
KeywordsREPLICATION / chromoshadow domain / complex / chromatin remodeler
Function / homology
Function and homology information


Factors involved in megakaryocyte development and platelet production / : / chromosome, subtelomeric region => GO:0099115 / SHREC complex / : / pericentric heterochromatin => GO:0005721 / RNA Polymerase I Promoter Escape / mating-type region heterochromatin / heterochromatin island / H3K9me3 modified histone binding ...Factors involved in megakaryocyte development and platelet production / : / chromosome, subtelomeric region => GO:0099115 / SHREC complex / : / pericentric heterochromatin => GO:0005721 / RNA Polymerase I Promoter Escape / mating-type region heterochromatin / heterochromatin island / H3K9me3 modified histone binding / regulatory ncRNA-mediated heterochromatin formation / chromosome, subtelomeric region / pericentric heterochromatin formation / nucleosome organization / rDNA heterochromatin / rDNA heterochromatin formation / ATP-dependent chromatin remodeler activity / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / nucleosome binding / pericentric heterochromatin / 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 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow 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 / Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Chromo-like domain superfamily / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / 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 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Chromo domain-containing protein 2 / Chromatin remodeling factor mit1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLeopold, K. / Schalch, T.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_139137 Switzerland
Swiss National Science FoundationPP00P3_163760_1 Switzerland
Swiss National Science FoundationPP00P3_172904 Switzerland
CitationJournal: Genes Dev. / Year: 2019
Title: Transcriptional gene silencing requires dedicated interaction between HP1 protein Chp2 and chromatin remodeler Mit1.
Authors: Leopold, K. / Stirpe, A. / Schalch, T.
History
DepositionFeb 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Chromo domain-containing protein 2
B: Chromo domain-containing protein 2
C: Chromatin remodeling factor mit1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2295
Polymers24,9923
Non-polymers2362
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-22 kcal/mol
Surface area11500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.053, 58.053, 139.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-1140-

HOH

21B-1148-

HOH

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Components

#1: Protein Chromo domain-containing protein 2


Mass: 7829.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: O42934
#2: 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: 9333.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Production host: Escherichia coli (E. coli)
References: UniProt: Q9P793, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL / 1,6-Hexanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.96 Å3/Da / Density % sol: 68.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7 / Details: 2.4 M sodium malonate, pH 7, 3% 1,6-hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 20, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.6→47.3 Å / Num. obs: 36873 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 18.55 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.037 / Rrim(I) all: 0.116 / Net I/σ(I): 16.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 16.2 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1830 / CC1/2: 0.88 / Rpim(I) all: 0.296 / Rrim(I) all: 0.837 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSJan 26, 2018data reduction
Aimless0.5.21data scaling
PHASER2.7.16phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E0B

1e0b


Resolution: 1.6→47.297 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.4
RfactorNum. reflection% reflection
Rfree0.1975 1893 5.14 %
Rwork0.1708 --
obs0.1721 36802 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→47.297 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 16 145 1865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011768
X-RAY DIFFRACTIONf_angle_d0.9912375
X-RAY DIFFRACTIONf_dihedral_angle_d15.2211090
X-RAY DIFFRACTIONf_chiral_restr0.06264
X-RAY DIFFRACTIONf_plane_restr0.007287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.25711330.21552434X-RAY DIFFRACTION100
1.64-1.68440.21591480.20342457X-RAY DIFFRACTION100
1.6844-1.7340.23891540.20192419X-RAY DIFFRACTION100
1.734-1.78990.23981270.1892455X-RAY DIFFRACTION100
1.7899-1.85390.231160.1992488X-RAY DIFFRACTION100
1.8539-1.92810.25691280.20962474X-RAY DIFFRACTION100
1.9281-2.01590.19811230.18242487X-RAY DIFFRACTION100
2.0159-2.12220.2341600.17262428X-RAY DIFFRACTION100
2.1222-2.25510.18831260.17212497X-RAY DIFFRACTION100
2.2551-2.42920.18241580.16942463X-RAY DIFFRACTION100
2.4292-2.67370.19571380.1782495X-RAY DIFFRACTION100
2.6737-3.06050.24171210.1842555X-RAY DIFFRACTION100
3.0605-3.85570.19231260.1612557X-RAY DIFFRACTION100
3.8557-47.31780.15491350.14742700X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -3.1694 Å / Origin y: 54.9965 Å / Origin z: 151.3108 Å
111213212223313233
T0.2009 Å20.0497 Å2-0.0109 Å2-0.1661 Å2-0.0037 Å2--0.1748 Å2
L0.8046 °2-0.8547 °20.1269 °2-1.7257 °2-0.6359 °2--0.7457 °2
S0.0844 Å °0.1595 Å °0.0234 Å °-0.1297 Å °-0.1226 Å °0.0088 Å °0.0779 Å °0.0093 Å °0.0301 Å °
Refinement TLS groupSelection details: all

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