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- PDB-7y7p: QDE-1 in complex with RNA template, RNA primer and AMPNPP -

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Basic information

Entry
Database: PDB / ID: 7y7p
TitleQDE-1 in complex with RNA template, RNA primer and AMPNPP
Components
  • RNA (5'-R(*GP*AP*A*CP*UP*AP*UP*GP*GP*UP*CP*GP*GP*A)-3')
  • RNA (5'-R(*UP*CP*CP*GP*AP*CP*C)-3')
  • RNA-dependent RNA polymerase
KeywordsRNA BINDING PROTEIN / RNA polymerase / QDE-1 / Complex / RdRP / AMPNPP
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
DI(HYDROXYETHYL)ETHER / Chem-ZAN / RNA / RNA (> 10) / RNA-dependent RNA polymerase
Similarity search - Component
Biological speciesNeurospora crassa (fungus)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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*A*CP*UP*AP*UP*GP*GP*UP*CP*GP*GP*A)-3')
D: RNA (5'-R(*UP*CP*CP*GP*AP*CP*C)-3')
E: RNA (5'-R(*GP*AP*A*CP*UP*AP*UP*GP*GP*UP*CP*GP*GP*A)-3')
J: RNA (5'-R(*UP*CP*CP*GP*AP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,13617
Polymers247,6456
Non-polymers1,49111
Water2,756153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16380 Å2
ΔGint-188 kcal/mol
Surface area76770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.949, 120.201, 114.857
Angle α, β, γ (deg.)90.000, 109.620, 90.000
Int Tables number4
Space group name H-MP1211

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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, 4 molecules CEDJ

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


Mass: 4526.756 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*C)-3')


Mass: 2156.347 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 164 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ZAN / 5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
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: Jan 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 70175 / % possible obs: 98.1 % / Redundancy: 4.8 % / Biso Wilson estimate: 58.61 Å2 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.029 / Rrim(I) all: 0.07 / Χ2: 0.813 / Net I/σ(I): 7.9 / Num. measured all: 337787
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.83.20.33367510.7140.1960.390.48594.4
2.8-2.913.40.29368250.8480.1670.340.5595.7
2.91-3.043.50.24768510.9070.1390.2850.57296.6
3.04-3.23.90.20369630.9470.110.2320.6497.5
3.2-3.44.70.16370420.980.0790.1820.84798.5
3.4-3.665.10.11370580.9920.0520.1240.88999.4
3.66-4.035.30.07871110.9960.0350.0860.93699.5
4.03-4.616.10.05371490.9980.0220.0570.91799.8
4.61-5.86.20.04571550.9990.0190.0490.83499.8
5.8-306.40.03972700.9990.0160.0430.95199.8

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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: 2.7→29.62 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.46 / Phase error: 29.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 3460 4.93 %
Rwork0.2227 66670 -
obs0.2242 70130 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.96 Å2 / Biso mean: 77.9054 Å2 / Biso min: 33.42 Å2
Refinement stepCycle: final / Resolution: 2.7→29.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14060 729 100 153 15042
Biso mean--63.99 61.59 -
Num. residues----1877
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.740.37431470.35242480262791
2.74-2.780.36321270.34712584271195
2.78-2.820.39281710.33942552272395
2.82-2.860.39111370.32692585272295
2.86-2.910.37121290.32092578270796
2.91-2.960.32441220.2992630275296
2.96-3.010.3211100.28772649275997
3.01-3.070.32851420.2762591273396
3.07-3.130.32851440.2632613275797
3.13-3.20.32061140.27112722283698
3.2-3.280.30191430.26342671281498
3.28-3.360.27231350.25512643277899
3.36-3.450.31771150.23472703281899
3.45-3.550.28451210.22762726284799
3.55-3.660.28651340.222527202854100
3.66-3.80.24271590.2062683284299
3.8-3.950.24951300.202527332863100
3.95-4.130.2541530.193726832836100
4.13-4.340.20451330.180627122845100
4.34-4.610.21641530.176527342887100
4.61-4.970.21261440.184226992843100
4.97-5.470.18331480.194227342882100
5.47-6.250.25851490.209627242873100
6.25-7.850.21271510.218827532904100
7.85-29.620.2061490.19432768291799
Refinement TLS params.Method: refined / Origin x: 53.8683 Å / Origin y: -4.7823 Å / Origin z: 136.1086 Å
111213212223313233
T0.3653 Å2-0.046 Å20.0496 Å2-0.4112 Å2-0.0098 Å2--0.4461 Å2
L0.1005 °20.02 °20.2619 °2-0.321 °20.1521 °2--1.3477 °2
S0.0914 Å °-0.0417 Å °0.1128 Å °0.0016 Å °-0.087 Å °0.0546 Å °0.0581 Å °-0.0363 Å °0.0078 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA390 - 1401
2X-RAY DIFFRACTION1allB394 - 1401
3X-RAY DIFFRACTION1allC-2 - 8
4X-RAY DIFFRACTION1allD1 - 7
5X-RAY DIFFRACTION1allE-2 - 8
6X-RAY DIFFRACTION1allJ2 - 7
7X-RAY DIFFRACTION1allG1 - 7
8X-RAY DIFFRACTION1allF1 - 245
9X-RAY DIFFRACTION1allM11
10X-RAY DIFFRACTION1allN11

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