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- EMDB-5144: Ab initio reconstruction of a poliovirus-receptor complex via the... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-5144 | |||||||||
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Title | Ab initio reconstruction of a poliovirus-receptor complex via the asymmetric random-model method | |||||||||
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![]() | Poliovirus-receptor complex: virus ![]() | |||||||||
![]() | random-model method / ab initio reconstruction / poliovirus-receptor complex. | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Sanz E / Stewart AB / Belnap DM | |||||||||
![]() | ![]() 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 Report | ![]() ![]() ![]() ![]() | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
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Download
Header (meta data in XML format) |
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Images |
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Archive directory |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire Poliovirus-receptor complex
Entire | Name: 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
Virus | Name: Human enterovirus C![]() ![]() 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 |
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Species | Species: ![]() ![]() |
Source (natural) | Host Species: ![]() ![]() |
Shell #1 | Name of element: VP1 VP2 VP3 / Diameter: 242 Å / T number (triangulation number): 1 |
-Experimental details
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Sample preparation
Specimen | Specimen state: Particle / Method: ![]() |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
![]() | Microscope: 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. |
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Electron gun | Electron source: FIELD EMISSION GUN![]() |
Lens | Magnification: 38000 X (nominal) / Imaging mode: BRIGHT FIELD![]() |
Specimen Holder | Holder: Eucentric / Model: GATAN LIQUID NITROGEN |
Camera | Detector: GENERIC FILM |
-Image acquisition
Image acquisition | 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. |
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Image processing
![]() | Method: ![]() 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) |
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3D reconstruction | Algorithm: 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 |