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- PDB-3avt: Structure of viral RNA polymerase complex 1 -

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Basic information

Entry
Database: PDB / ID: 3avt
TitleStructure of viral RNA polymerase complex 1
Components
  • Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase
  • RNA (5'-R(*AP*UP*CP*GP*CP*CP*A)-3')
KeywordsTRANSLATION / TRANSFERASE/RNA / RNA polymerase / TRANSFERASE-RNA complex
Function / homology
Function and homology information


protein-synthesizing GTPase / guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / response to antibiotic / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / GTPase activity / GTP binding ...protein-synthesizing GTPase / guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / response to antibiotic / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / GTPase activity / GTP binding / RNA binding / metal ion binding / plasma membrane / cytoplasm / cytosol
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, C-terminal / Translation elongation factor EFTu/EF1A, bacterial/organelle / Elongation factor Tu, domain 2 / Elongation factor Tu (EF-Tu), GTP-binding domain / : / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
3'-DEOXY-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)
synthetic construct (others)
Escherichia phage Qbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.607 Å
AuthorsTakeshita, D. / Tomita, K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Molecular basis for RNA polymerization by Q beta replicase
Authors: Takeshita, D. / Tomita, K.
History
DepositionMar 8, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references
Revision 1.2Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Nov 1, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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
T: RNA (5'-R(*AP*UP*CP*GP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6936
Polymers143,5982
Non-polymers1,0954
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-35 kcal/mol
Surface area53180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.120, 255.990, 101.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#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
Details: chimera of Elongation factor Ts, Elongation factor Tu and Q beta replicase
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) synthetic construct (others), (gene. exp.) Escherichia phage Qbeta (virus)
Production host: Escherichia coli (E. coli)
References: UniProt: P0A6P3, UniProt: P0A6N3, UniProt: Q8LTE0
#2: RNA chain RNA (5'-R(*AP*UP*CP*GP*CP*CP*A)-3')


Mass: 2180.371 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-GH3 / 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE


Type: RNA linking / Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.14 Å3/Da / Density % sol: 60.86 %
Crystal growMethod: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A
DetectorDate: Jun 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 54977 / Biso Wilson estimate: 43.73 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AGP

3agp


Resolution: 2.607→19.994 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7714 / SU ML: 0.41 / σ(F): 1.44 / Phase error: 29.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2884 2562 5.04 %
Rwork0.2252 48300 -
obs0.2284 50862 91.84 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.955 Å2 / ksol: 0.284 e/Å3
Displacement parametersBiso max: 148.97 Å2 / Biso mean: 64.6235 Å2 / Biso min: 11.12 Å2
Baniso -1Baniso -2Baniso -3
1--2.1638 Å20 Å2-0 Å2
2--6.1384 Å20 Å2
3----3.9746 Å2
Refinement stepCycle: LAST / Resolution: 2.607→19.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9287 85 64 59 9495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019616
X-RAY DIFFRACTIONf_angle_d1.35913035
X-RAY DIFFRACTIONf_chiral_restr0.0851474
X-RAY DIFFRACTIONf_plane_restr0.0051669
X-RAY DIFFRACTIONf_dihedral_angle_d18.0673626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6068-2.65680.3359440.245188592931
2.6568-2.71090.3087880.27861655174358
2.7109-2.76970.3461250.2992207233276
2.7697-2.8340.37871220.30432701282393
2.834-2.90470.34361420.31412907304999
2.9047-2.9830.3561860.288228333019100
2.983-3.07040.33221410.268929013042100
3.0704-3.16920.33411440.243829123056100
3.1692-3.2820.28421310.24829113042100
3.282-3.41270.31671540.237828893043100
3.4127-3.56720.28731550.226329063061100
3.5672-3.75410.30271610.222629063067100
3.7541-3.98760.28941440.200429083052100
3.9876-4.29270.24291910.187929163107100
4.2927-4.71950.27511590.181129093068100
4.7195-5.39070.27461570.200629643121100
5.3907-6.74810.30431540.235829843138100
6.7481-19.99490.22191640.19493006317098

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