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- PDB-3avw: Structure of viral RNA polymerase complex 4 -

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Basic information

Entry
Database: PDB / ID: 3avw
TitleStructure of viral RNA polymerase complex 4
Components
  • Elongation factor Ts, Elongation factor Tu, LINKER, Q beta replicase
  • RNA (5'-R(*AP*UP*CP*GP*UP*GP*GP*AP*CP*CP*CP*A)-3')
  • RNA (5'-R(*GP*GP*GP*UP*CP*CP*AP*C)-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 / RNA-dependent RNA polymerase activity / response to antibiotic / nucleotide binding / GTPase activity / GTP binding / RNA binding ...guanosine tetraphosphate binding / translation elongation factor activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / response to antibiotic / nucleotide binding / GTPase activity / GTP binding / RNA binding / metal ion binding / plasma membrane / 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 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / 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
3'-DEOXY-GUANOSINE-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: 2.602 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_asym_id / _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_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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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*C)-3')
T: RNA (5'-R(*AP*UP*CP*GP*UP*GP*GP*AP*CP*CP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3586
Polymers147,7713
Non-polymers5873
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-59 kcal/mol
Surface area53400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.020, 256.830, 101.570
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*C)-3')


Mass: 2541.577 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: RNA chain RNA (5'-R(*AP*UP*CP*GP*UP*GP*GP*AP*CP*CP*CP*A)-3')


Mass: 3811.336 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 3 types, 107 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GH3 / 3'-DEOXY-GUANOSINE-5'-TRIPHOSPHATE


Type: RNA linking / Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 3.09 Å3/Da / Density % sol: 60.19 %

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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: 55827 / Biso Wilson estimate: 44.34 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
Resolution: 2.602→19.987 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.8304 / SU ML: 0.36 / σ(F): 1.46 / Phase error: 24.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2525 2677 5.05 %
Rwork0.2012 50356 -
obs0.2038 53033 94.12 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.7 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 134.17 Å2 / Biso mean: 55.5328 Å2 / Biso min: 13.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.2025 Å20 Å2-0 Å2
2--3.8607 Å20 Å2
3----2.6582 Å2
Refinement stepCycle: LAST / Resolution: 2.602→19.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9287 419 33 104 9843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099956
X-RAY DIFFRACTIONf_angle_d1.28113563
X-RAY DIFFRACTIONf_chiral_restr0.0851548
X-RAY DIFFRACTIONf_plane_restr0.0051684
X-RAY DIFFRACTIONf_dihedral_angle_d17.733778
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.602-2.64920.3238570.2771953101035
2.6492-2.70010.33121050.27311898200368
2.7001-2.7550.32741460.27142540268692
2.755-2.81480.34281430.26462756289999
2.8148-2.88010.31241470.25042751289899
2.8801-2.95190.27311440.24742752289699
2.9519-3.03140.31071420.23872785292799
3.0314-3.12030.29641690.23182773294299
3.1203-3.22060.25591240.218527982922100
3.2206-3.33520.28131650.22527872952100
3.3352-3.46810.29041270.215428132940100
3.4681-3.62510.2541420.202128022944100
3.6251-3.81490.26871390.197727982937100
3.8149-4.05210.26151600.183528142974100
4.0521-4.3620.20981340.169228332967100
4.362-4.79540.20951500.156628422992100
4.7954-5.47680.22871680.174228152983100
5.4768-6.85370.22051600.209928803040100
6.8537-19.98810.21041550.174129663121100

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