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- PDB-7y7q: QDE-1 in complex with RNA template, RNA primer and 3'-dGTP -

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Basic information

Entry
Database: PDB / ID: 7y7q
TitleQDE-1 in complex with RNA template, RNA primer and 3'-dGTP
Components
  • RNA (5'-R(*GP*AP*AP*CP*UP*AP*CP*CP*GP*UP*CP*GP*GP*A)-3')
  • RNA (5'-R(*UP*CP*CP*GP*AP*CP*G)-3')
  • RNA-dependent RNA polymerase
KeywordsRNA BINDING PROTEIN / RNA polymerase / QDE-1 / Complex / RdRP / 3'-dGTP
Function / homology
Function and homology information


nuclear RNA-directed RNA polymerase complex / siRNA processing / RNA-directed RNA polymerase / RNA-directed RNA polymerase activity / GTP binding / RNA binding / ATP binding / metal ion binding / identical protein binding
Similarity search - Function
: / RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / RNA / RNA (> 10) / RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsCui, R.X. / Gan, J.H. / Ma, J.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31230041 China
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Structural insights into the dual activities of the two-barrel RNA polymerase QDE-1.
Authors: Cui, R. / Li, H. / Zhao, J. / Li, X. / Gan, J. / Ma, J.
History
DepositionJun 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
C: RNA (5'-R(*GP*AP*AP*CP*UP*AP*CP*CP*GP*UP*CP*GP*GP*A)-3')
D: RNA (5'-R(*UP*CP*CP*GP*AP*CP*G)-3')
E: RNA (5'-R(*GP*AP*AP*CP*UP*AP*CP*CP*GP*UP*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,63219
Polymers245,4475
Non-polymers2,18514
Water11,422634
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.211, 85.813, 101.581
Angle α, β, γ (deg.)102.560, 104.050, 94.060
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein RNA-dependent RNA polymerase


Mass: 117139.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neurospora crassa (fungus) / Gene: qde-1, GE21DRAFT_1027066, GE21DRAFT_4945 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y7G6, RNA-directed RNA polymerase

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RNA chain , 2 types, 3 molecules CED

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


Mass: 4485.748 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(*UP*CP*CP*GP*AP*CP*G)-3')


Mass: 2196.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 648 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: PEG 4000, 200 mM KCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Sep 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 151259 / % possible obs: 94.5 % / Redundancy: 3 % / Biso Wilson estimate: 33.28 Å2 / Rmerge(I) obs: 0.081 / Rpim(I) all: 0.052 / Rrim(I) all: 0.096 / Χ2: 2.183 / Net I/σ(I): 14.6 / Num. measured all: 455234
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.122.20.525141340.3680.3920.6591.13588
2.12-2.212.40.464145660.5030.3340.5751.16891.1
2.21-2.312.60.383149800.6810.270.471.24693.3
2.31-2.432.80.316150560.80.2160.3841.30494.5
2.43-2.582.90.243152430.9070.1620.2931.44595.2
2.58-2.783.10.169154250.9620.110.2021.65696.4
2.78-3.063.30.115155240.9840.0720.1362.04896.9
3.06-3.53.50.076155220.9930.0460.0892.8597.2
3.5-4.413.50.052155000.9960.0320.0613.56396.8
4.41-303.50.043153090.9960.0260.0513.45695.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2j7n

2j7n


Resolution: 2.05→29.31 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 24.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 7583 5.01 %
Rwork0.1961 143655 -
obs0.1976 151238 94.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.57 Å2 / Biso mean: 47.661 Å2 / Biso min: 20.17 Å2
Refinement stepCycle: final / Resolution: 2.05→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14743 482 143 634 16002
Biso mean--64.65 44.26 -
Num. residues----1880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.080.34442220.31943901412376
2.08-2.10.36732350.30734451468688
2.1-2.130.3092150.29984515473089
2.13-2.150.31082470.28514614486190
2.15-2.180.32062340.27974646488091
2.18-2.210.28912400.27284647488792
2.21-2.240.31632470.26494687493493
2.24-2.280.2942760.25544751502793
2.28-2.310.32482770.24314796507394
2.31-2.350.28492300.24384827505795
2.35-2.390.26692690.23944791506094
2.39-2.430.27752540.22984768502295
2.43-2.480.25722840.22384796508095
2.48-2.530.24872750.21724885516095
2.53-2.590.24022290.21354846507596
2.59-2.650.26482400.21364893513396
2.65-2.710.24092340.20894955518997
2.71-2.790.23292610.24874513597
2.79-2.870.23592580.1984930518897
2.87-2.960.23112600.20064922518297
2.96-3.070.24552640.20794975523997
3.07-3.190.23162440.20064931517597
3.19-3.330.23372980.18864897519597
3.33-3.510.21352630.18654943520697
3.51-3.730.19922980.17154916521497
3.73-4.020.18722620.16754932519497
4.02-4.420.17662720.15054882515496
4.42-5.060.18122380.15394889512796
5.06-6.360.19622390.17675084532399
6.36-29.310.19442180.17864711492992
Refinement TLS params.Method: refined / Origin x: 1.6849 Å / Origin y: 13.7075 Å / Origin z: 47.3721 Å
111213212223313233
T0.2488 Å2-0.0092 Å20.0205 Å2-0.2661 Å20.0208 Å2--0.262 Å2
L0.1549 °20.033 °20.0864 °2-0.2793 °20.0778 °2--0.1924 °2
S-0.0095 Å °0.0072 Å °-0.0183 Å °-0.0007 Å °-0.0336 Å °-0.0484 Å °0.0521 Å °0.0232 Å °0.0368 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA391 - 1402
2X-RAY DIFFRACTION1allA1501
3X-RAY DIFFRACTION1allB398 - 1370
4X-RAY DIFFRACTION1allC5 - 14
5X-RAY DIFFRACTION1allD1 - 7
6X-RAY DIFFRACTION1allE6 - 11
7X-RAY DIFFRACTION1allF1
8X-RAY DIFFRACTION1allX2001 - 2006
9X-RAY DIFFRACTION1allG1 - 3
10X-RAY DIFFRACTION1allS2 - 5104
11X-RAY DIFFRACTION1allH1
12X-RAY DIFFRACTION1allM11
13X-RAY DIFFRACTION1allN11

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