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Ab initio reconstruction of a poliovirus-receptor complex via the asymmetric random-model method

by single particle reconstruction, at 30 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.631, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.631, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5144
TitleAb initio reconstruction of a poliovirus-receptor complex via the asymmetric random-model method
MapPoliovirus-receptor complex
SamplePoliovirus-receptor complex
Keywordsrandom-model method, ab initio reconstruction, poliovirus-receptor complex.
AuthorsSanz E, Stewart AB, Belnap DM
DateDeposition: 2009-11-21, Header release: 2010-04-26, Map release: 2010-04-26, Last update: 2011-07-08
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.631, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.631, Made by UCSF CHIMERA

Supplemental images

EMDB figure
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Article
Citation - Primary
ArticleJ. Struct. Biol., Vol. 171, Issue 2, Page 216-22, Year 2010
TitleThe random-model method enables ab initio 3D reconstruction of asymmetric particles and determination of particle symmetry.
AuthorsEduardo Sanz-García, Aaron B Stewart, David M Belnap
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
KeywordsCryoelectron Microscopy (methods), Image Processing, Computer-Assisted (methods), Imaging, Three-Dimensional (methods), Models, Theoretical
LinksPII: S1047-8477(10)00094-8, DOI: 10.1016/j.jsb.2010.03.017, PubMed: 20353825, PMC: PMC2885456
Citation - #1
ArticlePROC.NAT.ACAD.SCI.USA, Vol. 97, Page 73-78, Year 2000
TitleThree-dimensional structure of poliovirus receptor bound to poliovirus
AuthorsBelnap DM, McDermott BM Jr, Filman DJ, Cheng N, Trus BL, Zuccola HJ, Racaniello VR, Hogle JM, Steven AC
Map
FileEMD-5144.map ( map file in CCP4 format, 94561 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:0.631 (by author), 0.631 (movie #1):
Minimum - Maximum: -1.78653 - 2.201
Average (Standard dev.): 0.0187361 (0.283488)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 287 287 287
Origin : -143 -143 -143
Limit : 143 143 143
Spacing : 287 287 287
Unit CellA = 528.08 A , B = 528.08 A , C = 528.08 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 1.84 A , Y = 1.84 A , Z = 1.84 A
CCP4 map header info
modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-143-143-143
NC/NR/NS287287287
start NC,NX/NR,NY/NS,NZ-143-143-143
NC,NX/NR,NY/NS,NZ287287287
D min/max/mean-1.7872.2010.019
Annotation DetailsPoliovirus-receptor complex
Supplement
Sample
NamePoliovirus-receptor complex
Number of Components2
Oligomeric State1 virus binds 60 receptors
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.
Component #1: virus - Poliovirus
Scientific nameHuman enterovirus C
Common NamePoliovirus
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.
Scientific Name of SpeciesHuman enterovirus C (NCBI Taxonomy: 138950)
Common Name of SpeciesPoliovirus
EmptyNo
EnvelopedNo
IsolateSEROTYPE
ClassVIRION
Natural SourceHost Species: Homo sapiens (NCBI Taxonomy: 9606)
Host Category: VERTEBRATES
ShellDiameter: 242 A
Name Element: VP1 VP2 VP3
T Number: 1
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
InstrumentNONE
Imaging
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.
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 38000 X,
Imaging ModeBRIGHT FIELD
Defocus600 nm - 2600 nm
Specimen Holder
HolderEucentric ( GATAN LIQUID NITROGEN )
Camera
DetectorFilm
Image Acquisition
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.
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmProjection matching
SoftwarePFT3DR, Bsoft
CTF CorrectionPhase-flipped
DetailsRandom-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 By Author30
Resolution MethodFSC at 0.5 cut-off
Single Particle
Number of Projections5626
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.
Download
Data from EMDB
Header (meta data in XML format)emd-5144.xml (8.5 KB)
Map dataemd_5144.map.gz (44.9 MB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5144
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 25.8 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.4 MB
Session file for UCSF-Chimera, 25.8 KB