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- PDB-1qln: STRUCTURE OF A TRANSCRIBING T7 RNA POLYMERASE INITIATION COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1qln
TitleSTRUCTURE OF A TRANSCRIBING T7 RNA POLYMERASE INITIATION COMPLEX
Components
  • BACTERIOPHAGE T7 RNA POLYMERASE
  • DNA (5- D (P*CP*TP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP* AP*TP*TP*A)-3)
  • DNA (5-D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3)
  • RNA (5- R(PPP*GP*GP*G)-3)
KeywordsNUCLEOTIDYLTRANSFERASE / T7 RNA POLYMERASE / PROTEIN/DNA/RNA
Function / homology
Function and homology information


DNA-templated viral transcription / mitochondrial promoter sequence-specific DNA binding / DNA-directed RNA polymerase complex / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription
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 / T7 RNA polymerase
Similarity search - Component
Biological speciesBACTERIOPHAGE T7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCheetham, G.M.T. / Steitz, T.A.
CitationJournal: Science / Year: 1999
Title: Structure of a Transcribing T7 RNA Polymerase Initiation Complex
Authors: Cheetham, G.M.T. / Steitz, T.A.
History
DepositionSep 1, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2000Provider: 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 ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BACTERIOPHAGE T7 RNA POLYMERASE
N: DNA (5-D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3)
R: RNA (5- R(PPP*GP*GP*G)-3)
T: DNA (5- D (P*CP*TP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP* AP*TP*TP*A)-3)


Theoretical massNumber of molelcules
Total (without water)112,0074
Polymers112,0074
Non-polymers00
Water8,773487
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-2.6 kcal/mol
Surface area50780 Å2
MethodPQS
Unit cell
Length a, b, c (Å)221.200, 73.600, 80.900
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 BACTERIOPHAGE T7 RNA POLYMERASE


Mass: 98984.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACTERIOPHAGE T7 (virus) / Plasmid: PAR1219 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: EMBL: 431189, UniProt: P00573*PLUS, DNA-directed RNA polymerase
#2: DNA chain DNA (5-D(P*TP*AP*AP*TP*AP*CP*GP*AP*CP*TP*CP*AP*CP*TP*A)-3) / NON-TEMPLATE STRAND


Mass: 5154.387 Da / Num. of mol.: 1 / Fragment: PROMOTER / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE T7 (virus)
#3: RNA chain RNA (5- R(PPP*GP*GP*G)-3)


Mass: 1150.619 Da / Num. of mol.: 1 / Fragment: TRANSCRIPT / Source method: obtained synthetically
#4: DNA chain DNA (5- D (P*CP*TP*CP*CP*CP*TP*AP*TP*AP*GP*TP*GP*AP*GP*TP*CP*GP*TP* AP*TP*TP*A)-3) / TEMPLATE STRAND


Mass: 6717.352 Da / Num. of mol.: 1 / Fragment: PROMOTER / Source method: obtained synthetically / Source: (synth.) BACTERIOPHAGE T7 (virus)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.8 Å3/Da / Density % sol: 58 %
Crystal growpH: 8.7 / Details: pH 8.70
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.3 mMT7 RNAP11
20.35 mMT7 promoter11
34 mMribonucleotides GTP11
44 mMuridine 5'-triphosphate11
54 mMcytidine 5'-triphosphate11
64 mMalpha, beta-methylene ATP11
715 mM11MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 51405 / % possible obs: 97.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 10.6
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.37 / % possible all: 95.7
Reflection
*PLUS
Num. obs: 51537
Reflection shell
*PLUS
% possible obs: 95.7 %

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Processing

Software
NameVersionClassification
CNS0.5refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CEZ

1cez


Resolution: 2.4→40 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2307 5 %RANDOM
Rwork0.223 ---
obs0.223 51475 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 47.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20 Å2
2---4.59 Å20 Å2
3---5.72 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6696 809 0 487 7992
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.7
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_it1.911.5
X-RAY DIFFRACTIONc_mcangle_it3.112
X-RAY DIFFRACTIONc_scbond_it3.12
X-RAY DIFFRACTIONc_scangle_it4.392.5
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 12 /
RfactorNum. reflection
Rfree0.47 215
Rwork0.45 3943
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

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