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- PDB-4q7j: Complex structure of viral RNA polymerase -

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Basic information

Entry
Database: PDB / ID: 4q7j
TitleComplex structure of viral RNA polymerase
Components
  • (Elongation factor ...) x 2
  • 30S ribosomal protein S1
  • Q beta replicase
KeywordsTRANSLATION/TRANSFERASE / RNA polymerase / RNA binding motif / RNA dependent RNA polymerization / TRANSLATION-TRANSFERASE complex
Function / homology
Function and homology information


guanyl-nucleotide exchange factor complex / positive regulation of cytoplasmic translation / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / negative regulation of cytoplasmic translation / guanyl-nucleotide exchange factor activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit ...guanyl-nucleotide exchange factor complex / positive regulation of cytoplasmic translation / protein-synthesizing GTPase / guanosine tetraphosphate binding / translational elongation / translation elongation factor activity / negative regulation of cytoplasmic translation / guanyl-nucleotide exchange factor activity / ribosomal small subunit assembly / cytosolic small ribosomal subunit / cytoplasmic translation / single-stranded RNA binding / structural constituent of ribosome / translation / RNA-directed RNA polymerase / response to antibiotic / viral RNA genome replication / nucleotide binding / RNA-directed RNA polymerase activity / GTPase activity / mRNA binding / GTP binding / magnesium ion binding / RNA binding / zinc ion binding / metal ion binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Elongation factor Ts, dimerisation 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. ...GTP Cyclohydrolase I; Chain A, domain 1 - #20 / Elongation factor Ts, dimerisation 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. / GTP Cyclohydrolase I; Chain A, domain 1 / Tetrahydropterin Synthase; Chain A / RNA-directed RNA polymerase, bacteriophage, catalytic domain / RdRp of RNA-containing bacteriophages catalytic domain profile. / : / Ribosomal protein S1 / Ribosomal protein S1-like / Ubiquitin-associated (UBA) domain / 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. / S1 domain profile. / Translation elongation factor EFTu-like, domain 2 / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Ribosomal protein S1-like RNA-binding domain / Helicase, Ruva Protein; domain 3 / S1 RNA binding domain / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / S1 domain / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Nucleic acid-binding, OB-fold / DNA/RNA polymerase superfamily / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Elongation factor Ts / Small ribosomal subunit protein bS1 / Elongation factor Tu 1 / RNA-directed RNA polymerase subunit beta / RNA-directed RNA polymerase subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Enterobacteria phage Qbeta (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsTakeshita, D.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Molecular insights into replication initiation by Q beta replicase using ribosomal protein S1.
Authors: Takeshita, D. / Yamashita, S. / Tomita, K.
History
DepositionApr 25, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor Ts
B: Elongation factor Tu 1
C: Q beta replicase
D: 30S ribosomal protein S1
E: Elongation factor Ts
F: Elongation factor Tu 1
G: Q beta replicase
H: 30S ribosomal protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)342,76012
Polymers342,3758
Non-polymers3844
Water4,558253
1
A: Elongation factor Ts
B: Elongation factor Tu 1
C: Q beta replicase
D: 30S ribosomal protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,3806
Polymers171,1884
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13330 Å2
ΔGint-111 kcal/mol
Surface area61600 Å2
MethodPISA
2
E: Elongation factor Ts
F: Elongation factor Tu 1
G: Q beta replicase
H: 30S ribosomal protein S1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,3806
Polymers171,1884
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-117 kcal/mol
Surface area62030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.190, 150.830, 189.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Elongation factor ... , 2 types, 4 molecules AEBF

#1: Protein Elongation factor Ts / EF-Ts


Mass: 30332.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tsf / Production host: Escherichia coli (E. coli) / References: UniProt: P0A6P1
#2: Protein Elongation factor Tu 1 / EF-Tu


Mass: 43209.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tufA / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE47

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Protein , 2 types, 4 molecules CGDH

#3: Protein Q beta replicase


Mass: 66305.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Qbeta (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8LTE0, UniProt: P14647*PLUS
#4: Protein 30S ribosomal protein S1


Mass: 31340.545 Da / Num. of mol.: 2 / Fragment: UNP residues 1-273
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: rpsA / Production host: Escherichia coli (E. coli) / References: UniProt: P0AG67

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Non-polymers , 2 types, 257 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.76 Å3/Da / Density % sol: 55.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris, 0.2M lithium sulfate, 20% PEG3350, pH 8.0, 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 270 / Detector: CCD / Date: Feb 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 84212 / Biso Wilson estimate: 43.49 Å2
Reflection shellResolution: 2.9→2.95 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.58 / % possible all: 86.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AGP

3agp


Resolution: 2.9→19.982 Å / FOM work R set: 0.7413 / SU ML: 0.6 / σ(F): 1.51 / Phase error: 32.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3088 4171 4.99 %
Rwork0.2553 --
obs0.258 83532 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 175.49 Å2 / Biso mean: 63.95 Å2 / Biso min: 6.88 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21096 0 20 253 21369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00321480
X-RAY DIFFRACTIONf_angle_d0.74429045
X-RAY DIFFRACTIONf_chiral_restr0.0533305
X-RAY DIFFRACTIONf_plane_restr0.0033778
X-RAY DIFFRACTIONf_dihedral_angle_d13.2947991
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9001-2.9330.40941500.37662519266997
2.933-2.96740.3641370.37492593273097
2.9674-3.00340.42331070.36052602270998
3.0034-3.04130.35621160.36042600271698
3.0413-3.08120.4311370.35262582271998
3.0812-3.12320.41551290.34852598272799
3.1232-3.16770.351230.33712629275299
3.1677-3.21480.41121290.32182624275399
3.2148-3.26480.35081310.32192590272199
3.2648-3.31810.38371610.31672622278399
3.3181-3.3750.371430.30122598274199
3.375-3.43610.33371330.2852635276899
3.4361-3.50190.33821320.27842664279699
3.5019-3.5730.34541430.27672641278499
3.573-3.65020.3341330.27272611274499
3.6502-3.73460.35861170.26332674279199
3.7346-3.82730.34691310.25672631276299
3.8273-3.930.31381480.25226572805100
3.93-4.04480.30911620.24062621278399
4.0448-4.17420.27851560.226926422798100
4.1742-4.32190.2721350.21826652800100
4.3219-4.49310.29641600.207226272787100
4.4931-4.69510.25661490.207726612810100
4.6951-4.93910.27851400.197926942834100
4.9391-5.24330.26461370.198726842821100
5.2433-5.63970.2451440.217826962840100
5.6397-6.19180.31521480.227226792827100
6.1918-7.05310.25931430.221827262869100
7.0531-8.75970.23881520.202627542906100
8.7597-19.98280.22191450.192628422987100

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