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- EMDB-2270: Average reconstruction of cryoEM poliovirus polymerase tubes with... -

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Basic information

Entry
Database: EMDB / ID: EMD-2270
TitleAverage reconstruction of cryoEM poliovirus polymerase tubes with (-32,6) helical symmetry
Map dataHelical reconstruction of wild-type poliovirus polymerase tubes n,l (1,0): -32, 5 n,l (0,1): 6, 30 Map has 2-fold symmetry around the helical axis. t= 170, u= 495 (l = 170n + 495m) dphi = 123.636364, dz = 6.071919
Sample
  • Sample: Average reconstruction of poliovirus polymerase tubes
  • Protein or peptide: polymerase
Keywordspoliovirus polymerase / virus replication / helical reconstruction / cryoEM
Biological speciesHuman poliovirus 1 Mahoney
Methodhelical reconstruction / cryo EM / Resolution: 16.0 Å
AuthorsWang J / Bullitt E
CitationJournal: J Mol Biol / Year: 2013
Title: Surface for catalysis by poliovirus RNA-dependent RNA polymerase.
Authors: Jing Wang / John M Lyle / Esther Bullitt /
Abstract: The poliovirus RNA-dependent RNA polymerase, 3Dpol, replicates the viral genomic RNA on the surface of virus-induced intracellular membranes. Macromolecular assemblies of 3Dpol form linear arrays of ...The poliovirus RNA-dependent RNA polymerase, 3Dpol, replicates the viral genomic RNA on the surface of virus-induced intracellular membranes. Macromolecular assemblies of 3Dpol form linear arrays of subunits that propagate along a strong protein-protein interaction called interface-I, as was observed in the crystal structure of wild-type poliovirus polymerase. These "filaments" recur with slight modifications in planar sheets and, with additional modifications that accommodate curvature, in helical tubes of the polymerase, by packing filaments together via a second set of interactions. Periodic variations of subunit orientations within 3Dpol tubes give rise to "ghost reflections" in diffraction patterns computed from electron cryomicrographs of helical arrays. The ghost reflections reveal that polymerase tubes are formed by bundles of four to five interface-I filaments, which are then connected to the next bundle of filaments with a perturbation of interface interactions between bundles. While enzymatically inactive polymerase is also capable of oligomerization, much thinner tubes that lack interface-I interactions between adjacent subunits are formed, suggesting that long-range allostery produces conformational changes that extend from the active site to the protein-protein interface. Macromolecular assemblies of poliovirus polymerase show repeated use of flexible interface interactions for polymerase lattice formation, suggesting that adaptability of polymerase-polymerase interactions facilitates RNA replication. In addition, the presence of a positively charged groove identified in polymerase arrays may help position and stabilize the RNA template during replication.
History
DepositionDec 27, 2012-
Header (metadata) releaseJan 16, 2013-
Map releaseJan 22, 2014-
UpdateJan 22, 2014-
Current statusJan 22, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 9.2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 9.2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2270.png

Downloads & links

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Map

FileDownload / File: emd_2270.map.gz / Format: CCP4 / Size: 115.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of wild-type poliovirus polymerase tubes n,l (1,0): -32, 5 n,l (0,1): 6, 30 Map has 2-fold symmetry around the helical axis. t= 170, u= 495 (l = 170n + 495m) dphi = 123.636364, dz = 6.071919
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 251 pix.
= 502. Å		2 Å/pix.
x 351 pix.
= 702. Å		2 Å/pix.
x 351 pix.
= 702. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.199999999999999 / Movie #1: 9.2
Minimum - Maximum-2.54001379 - 11.471538539999999
Average (Standard dev.)1.14350343 (±3.21037865)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-125
Dimensions351351251
Spacing351351251
CellA: 702.0 Å / B: 702.0 Å / C: 502.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z351351251
origin x/y/z0.0000.0000.000
length x/y/z702.000702.000502.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS00-125
NC/NR/NS351351251
D min/max/mean-2.54011.4721.144

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Supplemental data

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Sample components

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Entire : Average reconstruction of poliovirus polymerase tubes

EntireName: Average reconstruction of poliovirus polymerase tubes
Components
  • Sample: Average reconstruction of poliovirus polymerase tubes
  • Protein or peptide: polymerase

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Supramolecule #1000: Average reconstruction of poliovirus polymerase tubes

SupramoleculeName: Average reconstruction of poliovirus polymerase tubes / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 17.4 MDa

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Macromolecule #1: polymerase

MacromoleculeName: polymerase / type: protein_or_peptide / ID: 1 / Number of copies: 331 / Recombinant expression: Yes
Source (natural)Organism: Human poliovirus 1 Mahoney
Molecular weightTheoretical: 52.5 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pT5T-3D

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

GridDetails: Quantifoil
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 1, 2011
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: LN2 cooled / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 6.1 Å
Applied symmetry - Helical parameters - Δ&Phi: 67.5 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Software - Name: MRC, EMIP, Chimera

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Atomic model buiding 1

Initial modelPDB ID:

1ra6

SoftwareName: Chimera
RefinementSpace: REAL

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