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- EMDB-5560: CryoEM of Poliovirus Polymerase Tube, including Ghost Reflections -

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Basic information

Entry
Database: EMDB / ID: EMD-5560
TitleCryoEM of Poliovirus Polymerase Tube, including Ghost Reflections
Map dataHelical reconstruction of a tube of poliovirus polymerase, including ghost reflections
Sample
  • Sample: Oligomer of poliovirus polymerase; helical structure with ghost reflections included
  • Protein or peptide: poliovirus polymerase
Keywordspoliovirus polymerase / viral replication
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 releaseFeb 12, 2014-
UpdateApr 23, 2014-
Current statusApr 23, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 15.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 15.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 15.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5560.jpg

Downloads & links

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Map

FileDownload / File: emd_5560.map.gz / Format: CCP4 / Size: 13.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical reconstruction of a tube of poliovirus polymerase, including ghost reflections
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.4 Å/pix.
x 148 pix.
= 503.2 Å		3.4 Å/pix.
x 159 pix.
= 540.6 Å		3.4 Å/pix.
x 159 pix.
= 540.6 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: 3.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 15.5 / Movie #1: 15.5
Minimum - Maximum-34.0 - 62.0
Average (Standard dev.)1.82832026 (±11.531558990000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions159159148
Spacing159159148
CellA: 540.60004 Å / B: 540.60004 Å / C: 503.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.43.43.4
M x/y/z159159148
origin x/y/z0.0000.0000.000
length x/y/z540.600540.600503.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS159159148
D min/max/mean-34.00062.0001.828

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Supplemental data

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Sample components

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Entire : Oligomer of poliovirus polymerase; helical structure with ghost r...

EntireName: Oligomer of poliovirus polymerase; helical structure with ghost reflections included
Components
  • Sample: Oligomer of poliovirus polymerase; helical structure with ghost reflections included
  • Protein or peptide: poliovirus polymerase

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Supramolecule #1000: Oligomer of poliovirus polymerase; helical structure with ghost r...

SupramoleculeName: Oligomer of poliovirus polymerase; helical structure with ghost reflections included
type: sample / ID: 1000 / Oligomeric state: oligomer of 331 components / Number unique components: 1
Molecular weightTheoretical: 17.4 MDa / Method: 52.5 kD monomer

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Macromolecule #1: poliovirus polymerase

MacromoleculeName: poliovirus polymerase / type: protein_or_peptide / ID: 1 / Name.synonym: 3Dpol
Details: polymerase was oligomerized by incubation at 30C followed by incubation at 4C.
Number of copies: 331 / Oligomeric state: oligomer / Recombinant expression: Yes
Source (natural)Organism: Human poliovirus 1 Mahoney / Strain: Mahoney / synonym: poliovirus
Molecular weightTheoretical: 17.4 MDa
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 grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK I / Method: Blot for 3 sec before plunging

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Electron microscopy

MicroscopeFEI TECNAI 20
DateJan 1, 2011
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm
Sample stageSpecimen holder model: OTHER

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Image processing

Detailsn,l (1,0): -31, 8 n,l (0,1): 6, 40 t= -208, u= 1288 (l = -208n + 1288m)
Final reconstructionApplied symmetry - Helical parameters - Δz: 3.040994 Å
Applied symmetry - Helical parameters - Δ&Phi: 58.136646 °
Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Software - Name: EMIP, Chimera

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