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- PDB-4fwt: Complex structure of viral RNA polymerase form III -

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Basic information

Entry
Database: PDB / ID: 4fwt
TitleComplex structure of viral RNA polymerase form III
Components
  • Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase
  • RNA (5'-R(*C*CP*CP*UP*AP*CP*CP*C)-3')
  • RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3')
KeywordsTRANSLATION / TRANSFERASE/RNA / RNA polymerase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / response to antibiotic / RNA-dependent RNA polymerase activity / nucleotide binding / GTPase activity / GTP binding / RNA binding ...guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / response to antibiotic / RNA-dependent RNA polymerase activity / nucleotide binding / GTPase activity / GTP binding / RNA binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
RNA-directed RNA polymerase beta-chain / RNA replicase, beta-chain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / RNA-directed RNA polymerase, bacteriophage, catalytic domain ...RNA-directed RNA polymerase beta-chain / RNA replicase, beta-chain / Translation elongation factor EFTs/EF1B / Translation elongation factor EFTs/EF1B, dimerisation / Translation elongation factor Ts, conserved site / Elongation factor Ts, dimerisation domain superfamily / Elongation factor TS / Elongation factor Ts signature 1. / Elongation factor Ts signature 2. / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / UBA-like superfamily / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RNA / Elongation factor Tu / Elongation factor Ts / RNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli O157:H7 (bacteria)
Escherichia phage Qbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsTakeshita, D. / Tomita, K.
CitationJournal: Structure / Year: 2012
Title: Mechanism for template-independent terminal adenylation activity of Q beta replicase
Authors: Takeshita, D. / Yamashita, S. / Tomita, K.
History
DepositionJul 2, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _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

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase
G: RNA (5'-R(*C*CP*CP*UP*AP*CP*CP*C)-3')
T: RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,1046
Polymers146,5013
Non-polymers6033
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-44 kcal/mol
Surface area53290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.514, 255.047, 100.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase


Mass: 141417.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Escherichia phage Qbeta (virus)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A6P3, UniProt: P0A6N3, UniProt: Q8LTE0

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RNA chain , 2 types, 2 molecules GT

#2: RNA chain RNA (5'-R(*C*CP*CP*UP*AP*CP*CP*C)-3')


Mass: 2421.505 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized.
#3: RNA chain RNA (5'-R(*GP*GP*GP*UP*AP*GP*GP*G)-3')


Mass: 2661.649 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized.

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Non-polymers , 3 types, 11 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 30% PEG400, 0.2M calcium acetate, 0.1M HEPES, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2012
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 29292 / % possible obs: 90.2 % / Observed criterion σ(I): 0
Reflection shellResolution: 3.1→3.15 Å / % possible all: 90.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3avt

3avt


Resolution: 3.2→20 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.833 / SU B: 33.828 / SU ML: 0.544 / Cross valid method: THROUGHOUT / ESU R Free: 0.649 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3138 1370 5.1 %RANDOM
Rwork0.2448 ---
all0.24827 ---
obs0.24827 25474 90.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 98.648 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--4.25 Å20 Å2
3----4.16 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9287 253 34 8 9582
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0199771
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.95413276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.12151198
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.33423.831415
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.057151645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4311570
X-RAY DIFFRACTIONr_chiral_restr0.0870.21499
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217240
LS refinement shellResolution: 3.2→3.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.438 88 -
Rwork0.437 1511 -
obs--78.31 %

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