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- PDB-7y7r: QDE-1 in complex with DNA template, RNA primer and 3'-dGTP -

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Basic information

Entry
Database: PDB / ID: 7y7r
TitleQDE-1 in complex with DNA template, RNA primer and 3'-dGTP
Components
  • DNA (5'-D(*GP*AP*AP*CP*TP*AP*CP*CP*GP*TP*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 / DdRP / 3'-dGTP
Function / homology
Function and homology information


nuclear RNA-directed RNA polymerase complex / siRNA processing / RNA-directed RNA polymerase / RNA-dependent RNA polymerase activity / GTP binding / RNA binding / ATP binding / identical protein binding / metal ion binding
Similarity search - Function
RNA-dependent RNA polymerase, eukaryotic-type / RNA dependent RNA polymerase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / 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: 2.1 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: DNA (5'-D(*GP*AP*AP*CP*TP*AP*CP*CP*GP*TP*CP*GP*GP*A)-3')
D: RNA (5'-R(*UP*CP*CP*GP*AP*CP*G)-3')
E: DNA (5'-D(*GP*AP*AP*CP*TP*AP*CP*CP*GP*TP*CP*GP*GP*A)-3')
F: RNA (5'-R(*UP*CP*CP*GP*AP*CP*G)-3')
G: RNA (5'-R(*UP*CP*CP*GP*AP*CP*G)-3')
H: DNA (5'-D(*GP*AP*AP*CP*TP*AP*CP*CP*GP*TP*CP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,28319
Polymers253,7378
Non-polymers1,54611
Water9,116506
1
A: RNA-dependent RNA polymerase
B: RNA-dependent RNA polymerase
C: DNA (5'-D(*GP*AP*AP*CP*TP*AP*CP*CP*GP*TP*CP*GP*GP*A)-3')
D: RNA (5'-R(*UP*CP*CP*GP*AP*CP*G)-3')
E: DNA (5'-D(*GP*AP*AP*CP*TP*AP*CP*CP*GP*TP*CP*GP*GP*A)-3')
F: RNA (5'-R(*UP*CP*CP*GP*AP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,79717
Polymers247,2516
Non-polymers1,54611
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17490 Å2
ΔGint-133 kcal/mol
Surface area80470 Å2
MethodPISA
2
G: RNA (5'-R(*UP*CP*CP*GP*AP*CP*G)-3')
H: DNA (5'-D(*GP*AP*AP*CP*TP*AP*CP*CP*GP*TP*CP*GP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)6,4862
Polymers6,4862
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area2820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.366, 122.165, 114.921
Angle α, β, γ (deg.)90.000, 109.290, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein / DNA chain / RNA chain , 3 types, 8 molecules ABCEHDFG

#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*AP*CP*TP*AP*CP*CP*GP*TP*CP*GP*GP*A)-3')


Mass: 4289.806 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 517 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / 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: 2.65 Å3/Da / Density % sol: 53.53 %
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: Oct 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 143543 / % possible obs: 93.5 % / Redundancy: 4.6 % / Biso Wilson estimate: 35.78 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.036 / Rrim(I) all: 0.088 / Χ2: 1.91 / Net I/σ(I): 13.1 / Num. measured all: 660472
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.182.30.446116890.2510.3030.5440.86276.4
2.18-2.262.60.422129580.5550.2710.5060.99984.8
2.26-2.3730.378138210.6140.2260.4441.00890.1
2.37-2.493.50.349143550.7120.1990.4051.06994
2.49-2.6540.295146650.8450.1580.3371.14296
2.65-2.854.60.229149400.9450.1130.2561.31597.3
2.85-3.145.30.157150750.9820.0710.1721.53998.5
3.14-3.596.10.093152780.9960.0390.1012.03999.2
3.59-4.526.60.064153130.9980.0260.0692.99399.6
4.52-506.80.045154490.9990.0180.0482.75699.1

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Processing

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

2j7n


Resolution: 2.1→49.57 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.41 / Phase error: 28.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2491 7161 4.99 %
Rwork0.2066 136254 -
obs0.2087 143415 93.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 197.81 Å2 / Biso mean: 53.7715 Å2 / Biso min: 20.41 Å2
Refinement stepCycle: final / Resolution: 2.1→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14507 987 113 506 16113
Biso mean--53.81 44.27 -
Num. residues----1886
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 (%)
2.1-2.130.39021750.37443414358970
2.13-2.150.41112060.35143736394277
2.15-2.180.34511800.34063881406180
2.18-2.20.36892020.33764060426283
2.2-2.230.34382360.33164073430985
2.23-2.260.38592170.33384149436686
2.26-2.30.3781990.30324314451388
2.3-2.330.34282610.30134290455190
2.33-2.370.36052290.30114527475692
2.37-2.410.34412460.28554467471393
2.41-2.450.3132690.27714538480794
2.45-2.490.33872430.26954606484995
2.49-2.540.32552700.25754569483995
2.54-2.590.28512120.24774676488896
2.59-2.650.30772520.24034678493097
2.65-2.710.27612320.22384726495897
2.71-2.780.25752490.21094728497797
2.78-2.850.27012680.20784742501097
2.85-2.940.26432640.21564744500898
2.94-3.030.25782500.2144774502499
3.03-3.140.2752580.21464797505599
3.14-3.260.2682720.19774787505999
3.26-3.410.21892330.18724869510299
3.41-3.590.23162790.18174827510699
3.59-3.820.19332570.167448405097100
3.82-4.110.21252130.158948945107100
4.11-4.530.1822180.147448995117100
4.53-5.180.18622910.153948355126100
5.18-6.520.20642350.18514915515099
6.52-49.570.21412450.18934899514498
Refinement TLS params.Method: refined / Origin x: -41.8636 Å / Origin y: -4.8742 Å / Origin z: -27.3835 Å
111213212223313233
T0.2399 Å20.0227 Å20.0447 Å2-0.2973 Å20.0026 Å2--0.2819 Å2
L0.1244 °20.0263 °20.0486 °2-0.2137 °2-0.042 °2--0.3697 °2
S0.0453 Å °-0.0084 Å °0.1026 Å °0.0076 Å °-0.0281 Å °0.003 Å °-0.0448 Å °-0.021 Å °-0.0061 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA391 - 1371
2X-RAY DIFFRACTION1allB395 - 1403
3X-RAY DIFFRACTION1allC5 - 14
4X-RAY DIFFRACTION1allD1 - 7
5X-RAY DIFFRACTION1allE2 - 13
6X-RAY DIFFRACTION1allF3 - 7
7X-RAY DIFFRACTION1allG1 - 7
8X-RAY DIFFRACTION1allH8 - 14
9X-RAY DIFFRACTION1allI1 - 3
10X-RAY DIFFRACTION1allJ1 - 3
11X-RAY DIFFRACTION1allS1 - 609
12X-RAY DIFFRACTION1allM11
13X-RAY DIFFRACTION1allN11

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