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- PDB-2rf4: Crystal structure of the RNA Polymerase I subcomplex A14/43 -

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Basic information

Entry
Database: PDB / ID: 2rf4
TitleCrystal structure of the RNA Polymerase I subcomplex A14/43
Components(DNA-directed RNA polymerase I subunit RPA4) x 2
KeywordsTRANSFERASE / Transferase DNA/RNA / DNA-binding / Phosphorylation / RNA Polymerase I / Pol I / PolI / RPolI / Nuclear Protein / Nucleolar Protein / Transcription / DDRP / Rpb4/7 / Ribosome biogenesis / DNA-directed RNA polymerase / Nucleus
Function / homology
Function and homology information


RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / : ...RNA Polymerase I Transcription Initiation / regulation of cell size / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / nucleolar large rRNA transcription by RNA polymerase I / transcription initiation at RNA polymerase I promoter / transcription by RNA polymerase I / RNA polymerase I complex / transcription elongation by RNA polymerase I / : / ribosome biogenesis / nucleus
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / Rpa43, N-terminal ribonucleoprotein (RNP) domain / RNA polymerase Rpb7-like, N-terminal domain / RPA43, OB domain / RPA43 OB domain in RNA Pol I / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / RNA polymerase Rpb7-like , N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3390 / RNA polymerase I, subunit Rpa14, fungi / Yeast RNA polymerase I subunit RPA14 / Rpa43, N-terminal ribonucleoprotein (RNP) domain / RNA polymerase Rpb7-like, N-terminal domain / RPA43, OB domain / RPA43 OB domain in RNA Pol I / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Nucleic acid-binding proteins / Dna Ligase; domain 1 / Helix non-globular / Special / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase I subunit RPA43 / DNA-directed RNA polymerase I subunit RPA14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 Å
AuthorsGeiger, S.R. / Kuhn, C.D. / Cramer, P.
CitationJournal: Cell / Year: 2007
Title: Functional architecture of RNA polymerase I.
Authors: Claus-D Kuhn / Sebastian R Geiger / Sonja Baumli / Marco Gartmann / Jochen Gerber / Stefan Jennebach / Thorsten Mielke / Herbert Tschochner / Roland Beckmann / Patrick Cramer /
Abstract: Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron ...Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming.
History
DepositionSep 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed RNA polymerase I subunit RPA4
B: DNA-directed RNA polymerase I subunit RPA4
C: DNA-directed RNA polymerase I subunit RPA4
D: DNA-directed RNA polymerase I subunit RPA4
E: DNA-directed RNA polymerase I subunit RPA4
F: DNA-directed RNA polymerase I subunit RPA4


Theoretical massNumber of molelcules
Total (without water)101,6976
Polymers101,6976
Non-polymers00
Water00
1
A: DNA-directed RNA polymerase I subunit RPA4
B: DNA-directed RNA polymerase I subunit RPA4


Theoretical massNumber of molelcules
Total (without water)33,8992
Polymers33,8992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
MethodPISA
2
C: DNA-directed RNA polymerase I subunit RPA4
D: DNA-directed RNA polymerase I subunit RPA4


Theoretical massNumber of molelcules
Total (without water)33,8992
Polymers33,8992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
MethodPISA
3
E: DNA-directed RNA polymerase I subunit RPA4
F: DNA-directed RNA polymerase I subunit RPA4


Theoretical massNumber of molelcules
Total (without water)33,8992
Polymers33,8992
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)229.857, 63.942, 65.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DNA-directed RNA polymerase I subunit RPA4 / DNA-directed DNA-dependent RNA polymerase 36 kDa polypeptide / A43


Mass: 24223.096 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPA43, RRN12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: P46669, DNA-directed RNA polymerase
#2: Protein DNA-directed RNA polymerase I subunit RPA4 / DNA-directed RNA polymerase I 14 kDa polypeptide / A14


Mass: 9675.876 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RPA43, RRN12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIL / References: UniProt: P50106, DNA-directed RNA polymerase
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 18 % (w/v) PEG 3350, 350 mM potassium acetate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97848 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 1, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97848 Å / Relative weight: 1
ReflectionResolution: 3.1→30 Å / Num. all: 33804 / Num. obs: 33670 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rsym value: 0.077 / Net I/σ(I): 16.14
Reflection shellResolution: 3.1→3.25 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 4.97 / Num. unique all: 4457 / Rsym value: 0.399 / % possible all: 99.6

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXDphasing
CNS1.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.1→30 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.2854 1660 -
Rwork0.2524 --
all-33770 -
obs-33670 99.7 %
Refinement stepCycle: LAST / Resolution: 3.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5530 0 0 0 5530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.92202
X-RAY DIFFRACTIONo_bond_d0.008917

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