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- PDB-2ckz: X-ray structure of RNA polymerase III subcomplex C17-C25. -

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Basic information

Entry
Database: PDB / ID: 2ckz
TitleX-ray structure of RNA polymerase III subcomplex C17-C25.
Components
  • DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE
  • DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE
KeywordsTRANSFERASE / DNA-DIRECTED RNA POLYMERASE / MULTIPROTEIN COMPLEX / NUCLEOTIDYLTRANSFERASE / NUCLEAR PROTEIN / HYPOTHETICAL PROTEIN / EUKARYOTIC NUCLEIC ACID POLYMERASE / CLASS III GENE TRANSCRIPTION / TRANSCRIPTION / TRNA SYNTHESIS
Function / homology
Function and homology information


: / RNA Polymerase III Transcription Initiation From Type 2 Promoter / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / RNA polymerase III complex / transcription by RNA polymerase III / DNA-directed 5'-3' RNA polymerase activity / nucleotide binding / DNA binding ...: / RNA Polymerase III Transcription Initiation From Type 2 Promoter / termination of RNA polymerase III transcription / transcription initiation at RNA polymerase III promoter / tRNA transcription by RNA polymerase III / RNA polymerase III complex / transcription by RNA polymerase III / DNA-directed 5'-3' RNA polymerase activity / nucleotide binding / DNA binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Helix Hairpins - #870 / RNA Polymerase II, Rpb4 subunit / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / RNA polymerase Rpb7-like, N-terminal domain / DNA-directed RNA polymerase, subunit E/RPC8 / Growth Hormone; Chain: A; / Helix Hairpins / Rpb4/RPC9 superfamily ...Helix Hairpins - #870 / RNA Polymerase II, Rpb4 subunit / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / RNA polymerase Rpb7-like, N-terminal domain / DNA-directed RNA polymerase, subunit E/RPC8 / Growth Hormone; Chain: A; / Helix Hairpins / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase subunit Rpb7-like / HRDC-like superfamily / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Up-down Bundle / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase III subunit RPC8 / DNA-directed RNA polymerase III subunit RPC9
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsJasiak, A.J. / Armache, K.-J. / Martens, B. / Jansen, R.-P. / Cramer, P.
CitationJournal: Mol.Cell / Year: 2006
Title: Structural Biology of RNA Polymerase III: Subcomplex C17/-C25 X-Ray Structure and 11-Subunit Enzyme Model
Authors: Jasiak, A.J. / Armache, K.-J. / Martens, B. / Jansen, R.-P. / Cramer, P.
History
DepositionApr 24, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 5, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 650 HELIX
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: DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE
B: DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE
C: DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE
D: DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)87,6324
Polymers87,6324
Non-polymers00
Water0
1
A: DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE
B: DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)43,8162
Polymers43,8162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE
D: DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE


Theoretical massNumber of molelcules
Total (without water)43,8162
Polymers43,8162
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)138.230, 138.230, 247.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE / C17 / 18.6 KDA PROTEIN IN CCT3-CCT8 INTERGENIC REGION


Mass: 18637.150 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P47076, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE III 25 KD POLYPEPTIDE / C25


Mass: 25178.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PET21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P35718, DNA-directed RNA polymerase

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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: 3.89 Å3/Da / Density % sol: 68.37 %
Crystal growpH: 7.5 / Details: pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97894
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 21, 2005 / Details: BENT MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97894 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. obs: 21061 / % possible obs: 88.6 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.6 / % possible all: 91.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: SAD / Resolution: 3.2→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.3073 994 4.2 %
Rwork0.2359 --
obs0.2359 21002 88.9 %
Solvent computationBsol: 56.9684 Å2 / ksol: 0.248836 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.166 Å2-8.293 Å20 Å2
2---14.166 Å20 Å2
3---28.331 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 0 0 4386
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2WATER_REP.PARAM

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