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- PDB-3ayh: Crystal structure of the C17/25 subcomplex from S. pombe RNA Poly... -

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Basic information

Entry
Database: PDB / ID: 3ayh
TitleCrystal structure of the C17/25 subcomplex from S. pombe RNA Polymerase III
Components
  • DNA-directed RNA polymerase III subunit rpc8
  • DNA-directed RNA polymerase III subunit rpc9
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / transcription initiation at RNA polymerase III promoter / RNA polymerase III complex / DNA-directed RNA polymerase activity / nucleotide binding / chromatin / DNA binding / nucleus / cytosol
Similarity search - Function
RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / DNA-directed RNA polymerase, subunit E/RPC8 / Growth Hormone; Chain: A; / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily ...RNA Polymerase II, Rpb4 subunit / RNA polymerase Rpb7-like, N-terminal domain / RNA polymerase III, subunit Rpc25 / DNA-directed RNA polymerase III subunit RPC9 / RNA polymerase III subunit Rpc25 / DNA-directed RNA polymerase, subunit E/RPC8 / Growth Hormone; Chain: A; / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Rpb4/RPC9 superfamily / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase subunit Rpb7-like / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / Nucleic acid-binding proteins / Dna Ligase; domain 1 / 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 speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.193 Å
AuthorsEhara, H. / Sekine, S. / Yokoyama, S.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structure of the C17/25 subcomplex from Schizosaccharomyces pombe RNA polymerase III
Authors: Ehara, H. / Sekine, S. / Yokoyama, S.
History
DepositionMay 6, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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
A: DNA-directed RNA polymerase III subunit rpc9
B: DNA-directed RNA polymerase III subunit rpc8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9854
Polymers38,7932
Non-polymers1922
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-26 kcal/mol
Surface area17050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.400, 85.400, 93.270
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein DNA-directed RNA polymerase III subunit rpc9 / RNA polymerase III subunit C9 / RNA polymerase III subunit C17


Mass: 15524.620 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: rpc17, SPAPB1E7.10 / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: Q9C0Z9
#2: Protein DNA-directed RNA polymerase III subunit rpc8 / RNA polymerase III subunit C8 / RNA polymerase III subunit C25


Mass: 23268.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Strain: ATCC 38366 / 972 / Gene: rpc25, SPBC2G5.07c / Plasmid: pET-Duet1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 (DE3) / References: UniProt: O94285
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 1.3M Li2SO4, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 31, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.19→34.38 Å / Num. all: 20649 / Num. obs: 20649 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 6.837
Reflection shellResolution: 2.19→2.25 Å / Redundancy: 10 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 4 / Num. unique all: 1524 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALAdata processing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CKZ

2ckz


Resolution: 2.193→34.376 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8599 / SU ML: 0.25 / σ(F): 0 / Phase error: 20.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1042 5.23 %RANDOM
Rwork0.1904 ---
obs0.1927 19924 96.56 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.241 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 109.72 Å2 / Biso mean: 36.3408 Å2 / Biso min: 12.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.8736 Å2-0 Å2-0 Å2
2--0.8736 Å2-0 Å2
3----1.7472 Å2
Refinement stepCycle: LAST / Resolution: 2.193→34.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2572 0 10 161 2743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082635
X-RAY DIFFRACTIONf_angle_d1.0023555
X-RAY DIFFRACTIONf_chiral_restr0.066384
X-RAY DIFFRACTIONf_plane_restr0.004458
X-RAY DIFFRACTIONf_dihedral_angle_d14.912981
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1926-2.30820.27641590.20462543270292
2.3082-2.45280.24751510.20352571272295
2.4528-2.64210.27961480.20512636278495
2.6421-2.90790.26021430.1982676281996
2.9079-3.32840.22591480.18362728287698
3.3284-4.19220.21241470.17142797294499
4.1922-34.38020.22491460.195629313077100

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