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- PDB-6ju3: Structure of influenza D virus polymerase bound to cRNA promoter ... -

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Basic information

Entry
Database: PDB / ID: 6ju3
TitleStructure of influenza D virus polymerase bound to cRNA promoter in class 2
Components
  • Polymerase 3
  • Polymerase PB2
  • RNA (5'-R(P*AP*GP*CP*AP*UP*AP*AP*GP*CP*AP*GP*GP*AP*GP*A)-3')
  • RNA (5'-R(P*UP*CP*CP*UP*UP*GP*CP*UP*AP*CP*UP*GP*CP*U)-3')
  • RNA-directed RNA polymerase catalytic subunit
KeywordsVIRAL PROTEIN/RNA / influenza D virus / polymerase / cryo-EM / VIRAL PROTEIN / VIRAL PROTEIN-RNA complex / RNA BINDING PROTEIN
Function / homology
Function and homology information


ec:2.7.7.48: / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / nucleotide binding / RNA binding
RNA-directed RNA polymerase, negative-strand RNA virus / PA/PA-X superfamily / RdRp of negative ssRNA viruses with segmented genomes catalytic domain profile. / Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PA / Influenza RNA-dependent RNA polymerase subunit PB1 / Influenza RNA-dependent RNA polymerase subunit PB2 / Influenza RNA-dependent RNA polymerase subunit PB1
RNA-directed RNA polymerase catalytic subunit / Polymerase PB2 / Polymerase 3
Biological speciesInfluenza D virus
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPeng, Q. / Peng, R. / Qi, J. / Gao, G.F. / Shi, Y.
Funding supportChina , 1件
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08020100China
CitationJournal: To Be Published
Title: Structural insight into RNA synthesis by influenza D polymerase
Authors: Peng, Q. / Liu, Y. / Peng, R. / Wang, M. / Yang, W. / Song, H. / Chen, Y. / Liu, S. / Han, M. / Zhang, X. / Wang, P. / Yan, J. / Zhang, B. / Qi, J. / Deng, T. / Gao, G.F. / Shi, Y.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2019 / Release: Jun 12, 2019
RevisionDateData content typeProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release

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Assembly

Deposited unit
A: Polymerase 3
B: RNA-directed RNA polymerase catalytic subunit
C: Polymerase PB2
R: RNA (5'-R(P*UP*CP*CP*UP*UP*GP*CP*UP*AP*CP*UP*GP*CP*U)-3')
V: RNA (5'-R(P*AP*GP*CP*AP*UP*AP*AP*GP*CP*AP*GP*GP*AP*GP*A)-3')


Theoretical massNumber of molelcules
Total (without water)266,8955
Polymers266,8955
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein/peptide Polymerase 3 /


Mass: 83036.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus / Gene: P3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: K9LHJ4
#2: Protein/peptide RNA-directed RNA polymerase catalytic subunit


Mass: 86138.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus / Gene: PB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: K9LH03, EC: 2.7.7.48
#3: Protein/peptide Polymerase PB2


Mass: 88480.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza D virus / Gene: PB2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: K9LHF3
#4: RNA chain RNA (5'-R(P*UP*CP*CP*UP*UP*GP*CP*UP*AP*CP*UP*GP*CP*U)-3')


Mass: 4337.563 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: RNA chain RNA (5'-R(P*AP*GP*CP*AP*UP*AP*AP*GP*CP*AP*GP*GP*AP*GP*A)-3')


Mass: 4902.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Influenza D virus polymerase bound to cRNA promoter in mode B conformation
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5 / Source: RECOMBINANT
Molecular weightValue: 0.27 MDa / Experimental value: YES
Source (natural)Organism: Influenza D virus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Hive Five
Buffer solutionpH: 7.5
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimera11.1model fitting
9PHENIX1.11model refinement
10RELION2initial Euler assignment
11RELION2final Euler assignment
12RELION2classification
13RELION23D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 54216 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.00413992
f_angle_d0.918918
f_dihedral_angle_d13.9738519
f_chiral_restr0.0532079
f_plane_restr0.0062323

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