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- PDB-3avy: Structure of viral RNA polymerase complex 6 -

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Basic information

Entry
Database: PDB / ID: 3avy
TitleStructure of viral RNA polymerase complex 6
Components
  • Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase
  • RNA (5'-R(*AP*AP*CP*GP*AP*UP*UP*UP*UP*AP*UP*GP*GP*AP*CP*CP*CP*A)-3')
  • RNA (5'-R(*GP*GP*GP*UP*CP*CP*AP*UP*AP*AP*AP*AP*U)-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-CYTIDINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / 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: 2.616 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.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(*GP*GP*GP*UP*CP*CP*AP*UP*AP*AP*AP*AP*U)-3')
T: RNA (5'-R(*AP*AP*CP*GP*AP*UP*UP*UP*UP*AP*UP*GP*GP*AP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8486
Polymers151,3013
Non-polymers5473
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-67 kcal/mol
Surface area53310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.070, 257.220, 101.310
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
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

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RNA chain , 2 types, 2 molecules GT

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


Mass: 4165.550 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(*AP*AP*CP*GP*AP*UP*UP*UP*UP*AP*UP*GP*GP*AP*CP*CP*CP*A)-3')


Mass: 5717.450 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 91 molecules

#4: Chemical ChemComp-CH1 / 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#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


Mass: 18.015 Da / Num. of mol.: 88 / 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: 59.21 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A
DetectorDate: Oct 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 55288 / Biso Wilson estimate: 40.25 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: 2.616→19.993 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8301 / SU ML: 0.38 / σ(F): 1.42 / Phase error: 24.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2622 2739 5.08 %
Rwork0.214 51191 -
obs0.2164 53930 97.33 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.879 Å2 / ksol: 0.292 e/Å3
Displacement parametersBiso max: 150.16 Å2 / Biso mean: 51.4262 Å2 / Biso min: 13.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.5438 Å20 Å2-0 Å2
2--3.4364 Å20 Å2
3----1.8925 Å2
Refinement stepCycle: LAST / Resolution: 2.616→19.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9287 466 30 88 9871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910005
X-RAY DIFFRACTIONf_angle_d1.25713636
X-RAY DIFFRACTIONf_chiral_restr0.0871560
X-RAY DIFFRACTIONf_plane_restr0.0051686
X-RAY DIFFRACTIONf_dihedral_angle_d18.7793804
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.616-2.6610.3207660.2531385145153
2.661-2.70930.32021510.27572439259096
2.7093-2.76120.31931450.289525952740100
2.7612-2.81740.31771290.266926192748100
2.8174-2.87850.34881200.2626012721100
2.8785-2.94530.28271400.243725802720100
2.9453-3.01870.30351480.233226122760100
3.0187-3.10.28281320.236226102742100
3.1-3.19090.27981350.226926112746100
3.1909-3.29350.28371260.213326322758100
3.2935-3.41060.2611370.214826182755100
3.4106-3.54640.26591480.214825952743100
3.5464-3.70690.26651510.206426142765100
3.7069-3.9010.24621390.198726342773100
3.901-4.14330.21951660.18226072773100
4.1433-4.460.2151200.170826652785100
4.46-4.90280.22641530.1726312784100
4.9028-5.59860.27031250.208427012826100
5.5986-7.00290.27761440.234826742818100
7.0029-19.99320.24121640.212327682932100

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