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- PDB-4o9d: Structure of Dos1 propeller -

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Basic information

Entry
Database: PDB / ID: 4o9d
TitleStructure of Dos1 propeller
ComponentsRik1-associated factor 1
KeywordsGENE REGULATION / propeller / heterochromatin formation / Rik1 / Dos2 / transcription
Function / homology
Function and homology information


: / CLRC complex / pericentric heterochromatin => GO:0005721 / mating-type region heterochromatin / protein localization => GO:0008104 / meiotic telomere clustering / regulatory ncRNA-mediated heterochromatin formation / pericentric heterochromatin formation / chromatin => GO:0000785 / silent mating-type cassette heterochromatin formation ...: / CLRC complex / pericentric heterochromatin => GO:0005721 / mating-type region heterochromatin / protein localization => GO:0008104 / meiotic telomere clustering / regulatory ncRNA-mediated heterochromatin formation / pericentric heterochromatin formation / chromatin => GO:0000785 / silent mating-type cassette heterochromatin formation / subtelomeric heterochromatin formation / transcription repressor complex / negative regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat ...: / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Rik1-associated factor 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsKuscu, C. / Schalch, T. / Joshua-Tor, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: CRL4-like Clr4 complex in Schizosaccharomyces pombe depends on an exposed surface of Dos1 for heterochromatin silencing.
Authors: Kuscu, C. / Zaratiegui, M. / Kim, H.S. / Wah, D.A. / Martienssen, R.A. / Schalch, T. / Joshua-Tor, L.
History
DepositionJan 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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

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Assembly

Deposited unit
B: Rik1-associated factor 1
A: Rik1-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,40912
Polymers94,8152
Non-polymers59410
Water6,287349
1
B: Rik1-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6916
Polymers47,4081
Non-polymers2845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Rik1-associated factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,7186
Polymers47,4081
Non-polymers3105
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.150, 102.790, 95.100
Angle α, β, γ (deg.)90.00, 122.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rik1-associated factor 1 / Cryptic loci regulator 8 / De-localization of swi6 protein 1


Mass: 47407.684 Da / Num. of mol.: 2 / Fragment: Dos1WD
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: 972 / ATCC 24843 / Gene: raf1, clr8, cmc1, dos1, SPCC613.12c / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi5 / References: UniProt: O74910
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.64 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 291.15 K / pH: 7
Details: 50mM Tris-HCl pH=7.0, 0.9M di-sodium tartrate, 50mM Magnesium Chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9788
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2012
RadiationMonochromator: SELENIUM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2→45.87 Å / Num. obs: 65983 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 29.96 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.9
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 3.05 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2→45.87 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.61 / σ(F): 2 / Phase error: 25.06 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflection
Rfree0.2501 1734 2.63 %
Rwork0.2132 --
obs0.2142 65972 99.32 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.402 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso mean: 34.03 Å2
Baniso -1Baniso -2Baniso -3
1-9.4951 Å2-0 Å2-1.0276 Å2
2---9.6997 Å20 Å2
3---0.2045 Å2
Refinement stepCycle: LAST / Resolution: 2→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6084 0 37 349 6470
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016243
X-RAY DIFFRACTIONf_angle_d1.2098428
X-RAY DIFFRACTIONf_dihedral_angle_d13.2962188
X-RAY DIFFRACTIONf_chiral_restr0.08927
X-RAY DIFFRACTIONf_plane_restr0.0051078

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