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- PDB-1go3: Structure of an archeal homolog of the eukaryotic RNA polymerase ... -

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Basic information

Entry
Database: PDB / ID: 1go3
TitleStructure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex
Components
  • DNA-DIRECTED RNA POLYMERASE SUBUNIT E
  • DNA-DIRECTED RNA POLYMERASE SUBUNIT F
KeywordsTRANSFERASE / TRANSCRIPTION / DNA-DIRECTED RNA POLYMERASE
Function / homology
Function and homology information


DNA-directed RNA polymerase complex / DNA-templated transcription initiation / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / nucleotide binding / DNA binding / cytoplasm
Similarity search - Function
Helix Hairpins - #10 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo7 / HRDC domain / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / Helix Hairpins / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 ...Helix Hairpins - #10 / DNA-directed RNA polymerase subunit Rpo4 / DNA-directed RNA polymerase subunit Rpo7 / HRDC domain / RNA polymerase Rpb7-like, N-terminal domain / HRDC domain superfamily / DNA-directed RNA polymerase, subunit E/RPC8 / Helix Hairpins / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / S1 domain profile. / 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 / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / Nucleic acid-binding proteins / Dna Ligase; domain 1 / S1 domain / Helix non-globular / Special / DNA polymerase; domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit Rpo7 / DNA-directed RNA polymerase subunit Rpo4
Similarity search - Component
Biological speciesMETHANOCOCCUS JANNASCHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.75 Å
AuthorsTodone, F. / Brick, P. / Werner, F. / Weinzierl, R.O.J. / Onesti, S.
CitationJournal: Mol.Cell / Year: 2001
Title: Structure of an Archaeal Homolog of the Eukaryotic RNA Polymerase II Rpb4/Rpb7 Complex
Authors: Todone, F. / Brick, P. / Werner, F. / Weinzierl, R.O.J. / Onesti, S.
History
DepositionOct 17, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / entity_src_gen
Item: _citation.page_last / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._citation.page_last / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EB" AND "MB" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EB" AND "MB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: DNA-DIRECTED RNA POLYMERASE SUBUNIT E
F: DNA-DIRECTED RNA POLYMERASE SUBUNIT F
M: DNA-DIRECTED RNA POLYMERASE SUBUNIT E
N: DNA-DIRECTED RNA POLYMERASE SUBUNIT F


Theoretical massNumber of molelcules
Total (without water)67,1784
Polymers67,1784
Non-polymers00
Water5,909328
1
E: DNA-DIRECTED RNA POLYMERASE SUBUNIT E
F: DNA-DIRECTED RNA POLYMERASE SUBUNIT F


Theoretical massNumber of molelcules
Total (without water)33,5892
Polymers33,5892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
M: DNA-DIRECTED RNA POLYMERASE SUBUNIT E
N: DNA-DIRECTED RNA POLYMERASE SUBUNIT F


Theoretical massNumber of molelcules
Total (without water)33,5892
Polymers33,5892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)92.391, 92.391, 91.109
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.12195, -0.99217, 0.02686), (-0.99104, 0.12024, -0.05813), (0.05445, -0.0337, -0.99795)
Vector: 49.01272, 44.36161, 123.15306)

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Components

#1: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT E


Mass: 21246.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCOCCUS JANNASCHII (archaea)
Description: CO-EXPRESSED USING A BICISTRIONIC EXPRESSION STRATEGY
Plasmid: PGEX-2TK / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57840, DNA-directed RNA polymerase
#2: Protein DNA-DIRECTED RNA POLYMERASE SUBUNIT F


Mass: 12342.216 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) METHANOCOCCUS JANNASCHII (archaea)
Description: CO-EXPRESSED USING A BICISTRIONIC EXPRESSION STRATEGY
Plasmid: PGEX-2TX / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q60351, DNA-directed RNA polymerase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.9 Å3/Da / Density % sol: 55 %
Crystal growpH: 4.6
Details: 100 MM TRIS/ HCL 1.3-1.4 M AMMONIUM DIHYDROGEN MONOPHOSPHATE, pH 4.60
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMMES1droppH6.5
2100 mM1dropNaCl
310 mMbeta-mercaptoethanol1drop
420-25 mg/mlprotein1drop
51.3-1.6 M1reservoirNH4H2PO4
6100 mMTris-HCl1reservoirpH4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1
DetectorDetector: CCD / Date: Feb 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→27.8 Å / Num. obs: 76814 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 4.1
Reflection shellResolution: 1.75→1.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 3 / % possible all: 99.8
Reflection
*PLUS
Lowest resolution: 28 Å
Reflection shell
*PLUS
% possible obs: 99.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4data scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 1.75→27.8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2534087 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 3899 5.1 %RANDOM
Rwork0.217 ---
obs0.217 76811 99.6 %-
Solvent computationSolvent model: FLAT MODE / Bsol: 60.16 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 20.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å20 Å20 Å2
2---2.07 Å20 Å2
3---4.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.75→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4367 0 0 328 4695
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
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
LS refinement shellResolution: 1.75→1.86 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.273 643 5.1 %
Rwork0.244 12039 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.77

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