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- EMDB-5144: Ab initio reconstruction of a poliovirus-receptor complex via the... -

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Basic information

Entry
Database: EMDB / ID: EMD-5144
TitleAb initio reconstruction of a poliovirus-receptor complex via the asymmetric random-model method
Map dataPoliovirus-receptor complex
Sample
  • Sample: Poliovirus-receptor complex
  • Virus: Human enterovirus C
Keywordsrandom-model method / ab initio reconstruction / poliovirus-receptor complex.
Biological speciesHuman enterovirus C
Methodsingle particle reconstruction / cryo EM / Resolution: 30.0 Å
AuthorsSanz E / Stewart AB / Belnap DM
Citation
Journal: J Struct Biol / Year: 2010
Title: The random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry.
Authors: Eduardo Sanz-García / Aaron B Stewart / David M Belnap /
Abstract: Model-based, 3D reconstruction techniques depend on reliable starting models. We present an extension of the random-model method (RMM) that allows the ab initio generation of suitable starting models ...Model-based, 3D reconstruction techniques depend on reliable starting models. We present an extension of the random-model method (RMM) that allows the ab initio generation of suitable starting models directly from un-averaged, experimental images of asymmetric or symmetric particles. Therefore, the asymmetric RMM can also be used to determine point-group symmetry. The procedure is facilitated by the use of (a) variable angular step-sizes during iterative origin and orientation searches, (b) high numbers of particle images, and (c) highly defocused images. The method is inhibited by mixed-handedness orientation assignments and by particles with inconspicuous features. For symmetric particles, symmetric RMMs can overcome these deficiencies.
#1: Journal: PROC.NAT.ACAD.SCI.USA / Year: 2000
Title: Three-dimensional structure of poliovirus receptor bound to poliovirus
Authors: Belnap DM / McDermott BM Jr / Filman DJ / Cheng N / Trus BL / Zuccola HJ / Racaniello VR / Hogle JM / Steven AC
History
DepositionNov 21, 2009-
Header (metadata) releaseApr 26, 2010-
Map releaseApr 26, 2010-
UpdateJul 8, 2011-
Current statusJul 8, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.631
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.631
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5144.gif

emd_5144_1.tif

Downloads & links

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Map

FileDownload / File: emd_5144.map.gz / Format: CCP4 / Size: 88.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPoliovirus-receptor complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.84 Å/pix.
x 287 pix.
= 528.08 Å		1.84 Å/pix.
x 287 pix.
= 528.08 Å		1.84 Å/pix.
x 287 pix.
= 528.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.631 / Movie #1: 0.631
Minimum - Maximum-1.78653 - 2.201
Average (Standard dev.)0.0187361 (±0.283488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-143-143-143
Dimensions287287287
Spacing287287287
CellA=B=C: 528.08 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.841.841.84
M x/y/z287287287
origin x/y/z0.0000.0000.000
length x/y/z528.080528.080528.080
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-143-143-143
NC/NR/NS287287287
D min/max/mean-1.7872.2010.019

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Supplemental data

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Sample components

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Entire : Poliovirus-receptor complex

EntireName: Poliovirus-receptor complex
Components
  • Sample: Poliovirus-receptor complex
  • Virus: Human enterovirus C

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Supramolecule #1000: Poliovirus-receptor complex

SupramoleculeName: Poliovirus-receptor complex / type: sample / ID: 1000
Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to ...Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.
Oligomeric state: 1 virus binds 60 receptors / Number unique components: 2

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Supramolecule #1: Human enterovirus C

SupramoleculeName: Human enterovirus C / type: virus / ID: 1 / Name.synonym: Poliovirus
Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to ...Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.
NCBI-ID: 138950 / Sci species name: Human enterovirus C / Database: NCBI / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: Poliovirus
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: VP1 VP2 VP3 / Diameter: 242 Å / T number (triangulation number): 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DetailsD.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.
Image recordingCategory: CCD / Film or detector model: GENERIC FILM
Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to ...Details: D.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsD.M. Belnap, B.M. McDermott, Jr., D.J. Filman, N. Cheng, B.L. Trus, H.J. Zuccola, V.R. Racaniello, J.M. Hogle, A.C. Steven, Three-dimensional structure of poliovirus receptor bound to poliovirus, Proc. Natl. Acad. Sci. USA 97 (2000) 73-78.
CTF correctionDetails: Phase-flipped
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFT3DR, Bsoft
Details: Random-model method. Angular step-size was initially set to 20 deg. in the first iteration and gradually decreased by 0.19 deg. in each successive iteration, until a lower limit of 1 deg. was reached.
Number images used: 5626

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