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- PDB-3d1d: Hexagonal crystal structure of Tas3 C-terminal alpha motif -

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Basic information

Entry
Database: PDB / ID: 3d1d
TitleHexagonal crystal structure of Tas3 C-terminal alpha motif
ComponentsRNA-induced transcriptional silencing complex protein tas3
KeywordsNUCLEAR PROTEIN / all alpha motif / RITS complex immunoglobulin fold / Cell cycle / Chromosome partition / Nucleus / RNA-mediated gene silencing
Function / homology
Function and homology information


RITS complex / mating-type region heterochromatin / siRNA-mediated pericentric heterochromatin formation / regulatory ncRNA-mediated heterochromatin formation / chromosome, subtelomeric region / pericentric heterochromatin formation / silent mating-type cassette heterochromatin formation / spindle pole body / pericentric heterochromatin / chromosome segregation ...RITS complex / mating-type region heterochromatin / siRNA-mediated pericentric heterochromatin formation / regulatory ncRNA-mediated heterochromatin formation / chromosome, subtelomeric region / pericentric heterochromatin formation / silent mating-type cassette heterochromatin formation / spindle pole body / pericentric heterochromatin / chromosome segregation / heterochromatin formation / molecular adaptor activity / nucleus / cytoplasm
Similarity search - Function
Histone Acetyltransferase; Chain A - #40 / : / Tas3, C-terminal helical domains / Histone Acetyltransferase; Chain A / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA-induced transcriptional silencing complex protein tas3
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLi, H. / Patel, D.J.
CitationJournal: Mol.Cell / Year: 2009
Title: An alpha motif at Tas3 C terminus mediates RITS cis spreading and promotes heterochromatic gene silencing.
Authors: Li, H. / Motamedi, M.R. / Yip, C.K. / Wang, Z. / Walz, T. / Patel, D.J. / Moazed, D.
History
DepositionMay 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA-induced transcriptional silencing complex protein tas3
B: RNA-induced transcriptional silencing complex protein tas3
C: RNA-induced transcriptional silencing complex protein tas3
D: RNA-induced transcriptional silencing complex protein tas3
E: RNA-induced transcriptional silencing complex protein tas3
F: RNA-induced transcriptional silencing complex protein tas3


Theoretical massNumber of molelcules
Total (without water)83,6466
Polymers83,6466
Non-polymers00
Water3,171176
1
B: RNA-induced transcriptional silencing complex protein tas3
C: RNA-induced transcriptional silencing complex protein tas3


Theoretical massNumber of molelcules
Total (without water)27,8822
Polymers27,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-6 kcal/mol
Surface area11500 Å2
MethodPISA
2
E: RNA-induced transcriptional silencing complex protein tas3
F: RNA-induced transcriptional silencing complex protein tas3


Theoretical massNumber of molelcules
Total (without water)27,8822
Polymers27,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-7 kcal/mol
Surface area11390 Å2
MethodPISA
3
A: RNA-induced transcriptional silencing complex protein tas3

D: RNA-induced transcriptional silencing complex protein tas3


Theoretical massNumber of molelcules
Total (without water)27,8822
Polymers27,8822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+y+1,-x,z+1/31
Buried area1080 Å2
ΔGint-7 kcal/mol
Surface area11430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.891, 84.891, 165.724
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
RNA-induced transcriptional silencing complex protein tas3 / RITS protein tas3


Mass: 13940.937 Da / Num. of mol.: 6 / Fragment: UNP residues 426-545
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: tas3, SPBC83.03c / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta2(DE3) / References: UniProt: O94687
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.99 Å3/Da / Density % sol: 38.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG4000, 0.1 M Tris 7.5, 0.2 M KCl, 50 mM MgCl2, and 15% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 20741 / Num. obs: 19969 / % possible obs: 96.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 21.8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 12 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2052 / % possible all: 90

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3D1B

3d1b


Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1964 -random
Rwork0.206 ---
all-20741 --
obs-19940 86.7 %-
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5226 0 0 176 5402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.23721
X-RAY DIFFRACTIONc_bond_d0.007054
X-RAY DIFFRACTIONc_dihedral_angle_d18.49737
X-RAY DIFFRACTIONc_improper_angle_d0.82393

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