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- PDB-1h38: Structure of a T7 RNA polymerase elongation complex at 2.9A resolution -

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Basic information

Entry
Database: PDB / ID: 1h38
TitleStructure of a T7 RNA polymerase elongation complex at 2.9A resolution
Components
  • 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'
  • 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'
  • 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'
  • DNA-DIRECTED RNA POLYMERASEPolymerase
KeywordsTRANSFERASE / RNA POLYMERASE / T7 RNA POLYMERASE / ELONGATION COMPLEX / PROTEIN/DNA/RNA / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


DNA-templated viral transcription / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription / DNA binding
Similarity search - Function
T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / Helix Hairpins - #260 / Helix Hairpins - #280 / DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal ...T7 RNA polymerase; domain 1 / DNA-directed RNA polymerase, N-terminal domain / Helix Hairpins - #260 / Helix Hairpins - #280 / DNA-directed RNA polymerase, helix hairpin domain superfamily / DNA-directed RNA polymerase, N-terminal / DNA-directed RNA polymerase, N-terminal domain superfamily / DNA-directed RNA polymerase N-terminal / Bacteriophage-type RNA polymerase family active site signature 1. / DNA-directed RNA polymerase N-terminal / DNA-directed RNA polymerase, phage-type / : / DNA-dependent RNA polymerase / Bacteriophage-type RNA polymerase family active site signature 2. / Alpha-Beta Plaits - #370 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Helix Hairpins / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / T7 RNA polymerase
Similarity search - Component
Biological speciesBACTERIOPHAGE T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTahirov, T.H. / Temyakov, D. / Anikin, M. / Patlan, V. / McAllister, W.T. / Vassylyev, D.G. / Yokoyama, S.
CitationJournal: Nature / Year: 2002
Title: Structure of a T7 RNA Polymerase Elongation Complex at 2.9 A Resolution
Authors: Tahirov, T.H. / Temiakov, D. / Anikin, M. / Patlan, V. / Mcallister, W.T. / Vassylyev, D.G. / Yokoyama, S.
History
DepositionAug 24, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-DIRECTED RNA POLYMERASE
B: DNA-DIRECTED RNA POLYMERASE
C: DNA-DIRECTED RNA POLYMERASE
D: DNA-DIRECTED RNA POLYMERASE
E: 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'
F: 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'
G: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'
H: 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'
I: 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'
J: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'
K: 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'
L: 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'
M: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'
N: 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'
O: 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'
P: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)445,43316
Polymers445,43316
Non-polymers00
Water20,9331162
1
A: DNA-DIRECTED RNA POLYMERASE
E: 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'
F: 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'
G: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)111,3584
Polymers111,3584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: DNA-DIRECTED RNA POLYMERASE
H: 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'
I: 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'
J: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)111,3584
Polymers111,3584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: DNA-DIRECTED RNA POLYMERASE
K: 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'
L: 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'
M: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)111,3584
Polymers111,3584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: DNA-DIRECTED RNA POLYMERASE
N: 5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'
O: 5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'
P: 5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'


Theoretical massNumber of molelcules
Total (without water)111,3584
Polymers111,3584
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.907, 84.971, 202.003
Angle α, β, γ (deg.)90.36, 92.97, 109.94
Int Tables number1
Space group name H-MP1
DetailsEACH TETRAMER IS FORMED BY ONE MOLECULE OF PROTEININ COMPLEX WITH 2 MOLECULES OF DNA AND ONE MOLECULEOF RNA.

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Components

#1: Protein
DNA-DIRECTED RNA POLYMERASE / Polymerase


Mass: 98984.227 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE T7 (virus) / Plasmid: PAR1219 / Cell line (production host): DCAT4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00573, DNA-directed RNA polymerase
#2: DNA chain
5'-D(*GP*GP*GP*AP*AP*TP*CP*GP*AP*CP *AP*TP*CP*GP*CP*CP*GP*C)-3'


Mass: 5526.581 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE T7 (virus)
#3: RNA chain
5'-R(*AP*AP*CP*UP*GP*CP*GP*GP*CP*GP *AP*U)-3'


Mass: 3851.360 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE T7 (virus)
#4: DNA chain
5'-D(*GP*TP*CP*GP*AP*TP*TP*CP*CP*CP)-3'


Mass: 2995.967 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE T7 (virus)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1162 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Description: N-TERMINAL 266 RESIDUES AND ALL PROTRUDING SEGMENTS OF THE C-TERMINAL DOMAIN WERE REMOVED FROM THE SEARCH MODEL
Crystal growpH: 8.1
Details: 10% PEG 8000, 8% GLYCEROL, 5MM BETA-MERCAPTOETHANOL,100 MM TRIS BUFFER, PH8.1, pH 8.10
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 %PEG80001reservoir
310 %glycerol1reservoir
45 mMbeta-mercaptoethanol1reservoir
5100 mMTris1reservoirpH8.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.02
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 143689 / % possible obs: 94.2 % / Observed criterion σ(I): -1 / Redundancy: 3.4 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 14.7
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.9 / % possible all: 73.6
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 40 Å / Num. obs: 108303 / % possible obs: 98.1 % / Num. measured all: 348602 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3.08 Å / % possible obs: 94.5 % / Rmerge(I) obs: 0.335

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QLN

1qln


Resolution: 2.9→39.93 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3218106.53 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: DISORDERED REGIONS WERE REMOVED
RfactorNum. reflection% reflectionSelection details
Rfree0.284 5487 5.1 %RANDOM
Rwork0.236 ---
obs0.236 108303 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.0293 Å2 / ksol: 0.334118 e/Å3
Displacement parametersBiso mean: 71.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.55 Å29.46 Å26.73 Å2
2--6.2 Å23.56 Å2
3----2.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.9→39.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26984 2802 0 1162 30948
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it1.662
X-RAY DIFFRACTIONc_scangle_it2.642.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 879 5 %
Rwork0.299 16822 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 40 Å / % reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09
LS refinement shell
*PLUS
Highest resolution: 2.9 Å

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