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

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Entry
Database: EMDB / ID: EMD-5144
TitleAb initio reconstruction of a poliovirus-receptor complex via the asymmetric random-model method
Map data
SamplePoliovirus-receptor complex:
virus
Keywordsrandom-model method / ab initio reconstruction / poliovirus-receptor complex.
Biological speciesHuman enterovirus C (Poliovirus)
Methodsingle particle reconstruction / cryo EM / Resolution: 30 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
Validation ReportSummary, Full report, XML, About validation report
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

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)
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
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
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.
Number of components: 2 / Oligomeric State: 1 virus binds 60 receptors

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Component #1: virus, Human enterovirus C

VirusName: Human enterovirus C / a.k.a: Poliovirus / Class: VIRION
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.
Empty: No / Enveloped: No / Isolate: SEROTYPE
SpeciesSpecies: Human enterovirus C (Poliovirus)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: VP1 VP2 VP3 / Diameter: 242 Å / T number (triangulation number): 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG
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 gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensMagnification: 38000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 600 - 2600 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: GENERIC FILM

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Image acquisition

Image acquisitionDetails: 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.

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 5626
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.
Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: PFT3DR, Bsoft / CTF correction: Phase-flipped
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.
Resolution: 30 Å / Resolution method: FSC 0.5

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