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- PDB-9jkd: Crystal structure of Aspergillus fumigatus polymycovirus 1 ployme... -

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Basic information

Entry
Database: PDB / ID: 9jkd
TitleCrystal structure of Aspergillus fumigatus polymycovirus 1 ploymerase elongation complex
Components
  • RNA (30-MER)
  • RNA (5'-R(P*GP*GP*AP*UP*AP*UP*AP*AP*U)-3')
  • RNA dependent RNA polymerase
KeywordsVIRAL PROTEIN/RNA / polymerase-RNA / elongation / VIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding
Similarity search - Function
RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / RNA dependent RNA polymerase
Similarity search - Component
Biological speciesAspergillus fumigatus tetramycovirus 1
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsJia, H. / Gong, P.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0507200 China
National Natural Science Foundation of China (NSFC)32300139 China
CitationJournal: Sci Adv / Year: 2025
Title: An evolutionarily unique viral RdRP suggests a common dual-function feature of the priming element.
Authors: Jia, H. / Liu, S. / Rao, G. / Liu, Q. / Wu, J. / Cao, S. / Gong, P.
History
DepositionSep 15, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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 (30-MER)
C: RNA (5'-R(P*GP*GP*AP*UP*AP*UP*AP*AP*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6015
Polymers89,4173
Non-polymers1842
Water7,927440
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-39 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.270, 118.270, 136.942
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein RNA dependent RNA polymerase


Mass: 76913.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus fumigatus tetramycovirus 1 / Gene: RdRP / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: A0A0H5BRR0
#2: RNA chain RNA (30-MER)


Mass: 9622.776 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*GP*GP*AP*UP*AP*UP*AP*AP*U)-3')


Mass: 2880.774 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 54.07 %
Crystal growTemperature: 289 K / Method: evaporation
Details: potassium acetate, pentaerythritol propoxylate (5/4 PO/OH)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 41675 / % possible obs: 100 % / Redundancy: 25.8 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.013 / Rrim(I) all: 0.066 / Χ2: 0.943 / Net I/σ(I): 11.7 / Num. measured all: 1073844
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.34-2.4223.80.59341140.9640.1230.6050.931100
2.42-2.5226.70.44440860.9820.0870.4530.945100
2.52-2.6425.90.33441020.9890.0670.3410.919100
2.64-2.77270.23740890.9940.0460.2420.947100
2.77-2.95270.15541330.9970.030.1580.917100
2.95-3.1825.70.09241350.9990.0180.0940.919100
3.18-3.526.20.05741510.9990.0110.0580.951100
3.5-4260.03841790.9990.0080.0390.954100
4-5.0425.50.029423210.0060.030.918100
5.04-50240.028445410.0060.0291.02599.9

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Processing

Software
NameVersionClassification
PHENIX1.19refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Cyro-EM structure of AfuPmV-1 N85

Resolution: 2.34→27.32 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2167 2081 5.01 %
Rwork0.1732 39424 -
obs0.1754 41505 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.03 Å2 / Biso mean: 33.0401 Å2 / Biso min: 9.71 Å2
Refinement stepCycle: final / Resolution: 2.34→27.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5183 468 12 440 6103
Biso mean--51.32 33.97 -
Num. residues----694
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.34-2.390.28141420.207325892731100
2.39-2.450.24241410.192625782719100
2.45-2.520.27191340.185525962730100
2.52-2.590.26861440.196625672711100
2.59-2.680.26971320.185526162748100
2.68-2.770.23781190.1926022721100
2.77-2.890.23581410.198726212762100
2.89-3.020.26691400.193925982738100
3.02-3.180.28281330.197226292762100
3.18-3.370.25431280.188126172745100
3.37-3.630.19251490.172526232772100
3.63-40.19261550.156426332788100
4-4.570.17731570.140926442801100
4.57-5.750.16571260.148627212847100
5.75-27.320.1811400.1652790293098

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