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- PDB-7y7t: QDE-1 in complex with 12nt DNA template, ATP and 3'-dGTP -

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Basic information

Entry
Database: PDB / ID: 7y7t
TitleQDE-1 in complex with 12nt DNA template, ATP and 3'-dGTP
Components
  • DNA (5'-D(*GP*AP*G*AP*GP*AP*CP*CP*TP*TP*TP*T)-3')
  • RNA (5'-R(P*AP*AP*AP*G)-3')
  • RNA-dependent RNA polymerase
KeywordsRNA BINDING PROTEIN / RNA polymerase / QDE-1 / Complex / no primer / ATP / 3'-dGTP
Function / homology
Function and homology information


regulatory ncRNA-mediated gene silencing / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / RNA binding / identical protein binding / metal ion binding
Similarity search - Function
RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

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Assembly

Deposited unit
A: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
C: DNA (5'-D(*GP*AP*G*AP*GP*AP*CP*CP*TP*TP*TP*T)-3')
D: RNA (5'-R(P*AP*AP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)240,39611
Polymers239,2444
Non-polymers1,1527
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17030 Å2
ΔGint-120 kcal/mol
Surface area79460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.505, 85.790, 101.280
Angle α, β, γ (deg.)102.380, 103.410, 94.130
Int Tables number1
Space group name H-MP1

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Components

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Protein / DNA chain / RNA chain , 3 types, 4 molecules ABCD

#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
#2: DNA chain DNA (5'-D(*GP*AP*G*AP*GP*AP*CP*CP*TP*TP*TP*T)-3')


Mass: 3677.415 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*AP*AP*AP*G)-3')


Mass: 1287.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 166 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3 / Details: peg4000, 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 300 mm CCD / Detector: CCD / Date: Jan 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 78997 / % possible obs: 89 % / Redundancy: 5.4 % / Biso Wilson estimate: 48.47 Å2 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.05 / Rrim(I) all: 0.13 / Χ2: 1.331 / Net I/σ(I): 8.2 / Num. measured all: 427186
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.592.90.4562510.6160.2660.5261.1370.3
2.59-2.693.20.38570500.8170.2140.4431.18979.8
2.69-2.823.70.32973820.910.1710.3721.14583.1
2.82-2.964.40.29283120.940.1420.3261.13693.5
2.96-3.155.20.25984550.9640.1180.2861.20495.3
3.15-3.395.90.20584340.9810.0880.2241.2595
3.39-3.736.30.15979300.9870.0660.1731.4789.5
3.73-4.276.90.11586260.9910.0460.1241.39297.1
4.27-5.3870.09282250.9930.0360.0991.31492.9
5.38-307.30.08483320.9940.0330.091.5993.9

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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: 2.5→29.94 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2566 3956 5.01 %
Rwork0.221 74947 -
obs0.2228 78903 88.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 187.12 Å2 / Biso mean: 71.7085 Å2 / Biso min: 16.37 Å2
Refinement stepCycle: final / Resolution: 2.5→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14874 256 67 159 15356
Biso mean--78.82 50.4 -
Num. residues----1880
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.530.36181100.33121946205664
2.53-2.570.3736990.32572070216969
2.57-2.60.40121220.30782228235072
2.6-2.640.32051240.29722256238077
2.64-2.670.34241290.28592464259381
2.67-2.710.37971440.27542489263382
2.71-2.760.3241310.27532530266185
2.76-2.80.31511140.26972539265383
2.8-2.850.3231270.27262507263483
2.85-2.90.29541580.2762847300596
2.9-2.960.3251290.2742867299695
2.96-3.020.33471510.26372942309396
3.02-3.080.32871330.26172892302596
3.08-3.150.28181670.24732854302195
3.15-3.230.26171390.24462860299995
3.23-3.320.28831520.24122879303195
3.32-3.420.28131660.24232841300794
3.42-3.530.25971620.23392753291592
3.53-3.650.24221470.21792656280388
3.65-3.80.24061690.21062725289490
3.8-3.970.23061500.21062898304897
3.97-4.180.25491290.19232977310697
4.18-4.440.23081460.1852880302696
4.44-4.780.21681280.18622924305295
4.79-5.260.23151290.18912767289692
5.26-6.020.23441940.2152682287691
6.02-7.560.25661630.212895305896
7.57-29.940.17881440.18012779292392
Refinement TLS params.Method: refined / Origin x: 1.9909 Å / Origin y: 15.2595 Å / Origin z: 47.948 Å
111213212223313233
T0.1749 Å2-0.0015 Å20.034 Å2-0.1688 Å20.0203 Å2--0.174 Å2
L0.3328 °20.1541 °20.0759 °2-0.3457 °20.1248 °2--0.0845 °2
S-0.064 Å °0.0829 Å °-0.0455 Å °-0.0809 Å °0.0187 Å °-0.0899 Å °-0.0212 Å °-0.0303 Å °-0.013 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA391 - 1402
2X-RAY DIFFRACTION1allB396 - 1380
3X-RAY DIFFRACTION1allC4 - 12
4X-RAY DIFFRACTION1allJ11
5X-RAY DIFFRACTION1allK1 - 201
6X-RAY DIFFRACTION1allF1 - 5
7X-RAY DIFFRACTION1allD0 - 3
8X-RAY DIFFRACTION1allE1

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