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- EMDB-9887: Structure of influenza D virus polymerase bound to cRNA promoter ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9887
TitleStructure of influenza D virus polymerase bound to cRNA promoter in class 1
Map data
SampleInfluenza D virus polymerase bound to cRNA promoter in mode A conformation
  • Polymerase 3
  • RNA-directed RNA polymerase catalytic subunit
  • Polymerase PB2
  • (nucleic-acidNucleic acid) x 2
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsPeng Q / Peng R / Qi J / Gao GF / Shi Y
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 GF / Shi Y
Validation ReportPDB-ID: 6ju2

SummaryFull reportAbout validation report
DateDeposition: Apr 12, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ju2
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9887.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 180 pix.
= 244.8 Å
1.36 Å/pix.
x 180 pix.
= 244.8 Å
1.36 Å/pix.
x 180 pix.
= 244.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.022 / Movie #1: 0.04
Minimum - Maximum-0.32910034 - 0.5403177
Average (Standard dev.)0.0004422706 (±0.013163127)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 244.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z244.800244.800244.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.3290.5400.000

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Supplemental data

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Sample components

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Entire Influenza D virus polymerase bound to cRNA promoter in mode A con...

EntireName: Influenza D virus polymerase bound to cRNA promoter in mode A conformation
Number of components: 6

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Component #1: protein, Influenza D virus polymerase bound to cRNA promoter in m...

ProteinName: Influenza D virus polymerase bound to cRNA promoter in mode A conformation
Recombinant expression: No
MassExperimental: 270 kDa
SourceSpecies: Influenza D virus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm) / Cell of expression system: High five

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Component #2: protein, Polymerase 3

ProteinName: Polymerase 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 83.036086 kDa
SourceSpecies: Influenza D virus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #3: protein, RNA-directed RNA polymerase catalytic subunit

ProteinName: RNA-directed RNA polymerase catalytic subunit / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 86.138844 kDa
SourceSpecies: Influenza D virus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #4: protein, Polymerase PB2

ProteinName: Polymerase PB2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 88.480484 kDa
SourceSpecies: Influenza D virus
Source (engineered)Expression System: Spodoptera frugiperda (fall armyworm)

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Component #5: nucleic-acid, RNA (5'-R(P*UP*CP*CP*UP*UP*GP*CP*UP*AP*CP*UP*GP*CP*...

nucleic acidName: RNA (5'-R(P*UP*CP*CP*UP*UP*GP*CP*UP*AP*CP*UP*GP*CP*U)-3')
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
UCCUUGCUAC UGCU
MassTheoretical: 4.337563 kDa
SourceSpecies: synthetic construct (others)

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Component #6: nucleic-acid, RNA (5'-R(P*AP*GP*CP*AP*UP*AP*AP*GP*CP*AP*GP*GP*AP*...

nucleic acidName: RNA (5'-R(P*AP*GP*CP*AP*UP*AP*AP*GP*CP*AP*GP*GP*AP*GP*A)-3')
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AGCAUAAGCA GGAGA
MassTheoretical: 4.902042 kDa
SourceSpecies: synthetic construct (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.8 mg/mL / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 379512
3D reconstructionSoftware: RELION / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Output model

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