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Pseudo-atomic model of a fiberless isometric variant of bacteriophage phi29

by single particle (icosahedral) reconstruction, at 7.9 A resolution

Movie

Orientation:

#1: Biological unit as complete icosahedral assembly, Made by Jmol

#2: Biological unit as icosahedral pentamer, Made by Jmol

#3: Biological unit as icosahedral 23 hexamer, Made by Jmol

#4: Depositted structure unit, Made by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1116, Made by Jmol

#6: Superimposing with simplified surface model of EM map, EMDB-1120, Made by Jmol

#7: Superimposing with EM 3D map: EMDB-1120, Made by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 1yxn
TitlePseudo-atomic model of a fiberless isometric variant of bacteriophage phi29
DescriptorMajor head protein
KeywordsVirus, phi29, capsid, icosahedral virus capsid, hk97 fold, phage, bacterial immuno-globulin, BIG2, Icosahedral virus
AuthorsMorais, M.C., Choi, K.H., Koti, J.S., Chipman, P.R., Anderson, D.L., Rossmann, M.G.
DateDeposition: 2005-02-22, Release: 2005-04-26
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Biological unit as complete icosahedral assembly, Made by Jmol

#2: Biological unit as icosahedral pentamer, Made by Jmol

#3: Biological unit as icosahedral 23 hexamer, Made by Jmol

#4: Depositted structure unit, Made by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-1116, Made by Jmol

#6: Superimposing with simplified surface model of EM map, EMDB-1120, Made by Jmol

#7: Superimposing with EM 3D map: EMDB-1120, Made by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries

EMDB-1116

CiteFit

EMDB-1120

CiteFit

Cite: data citing same article

Fit: target map of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - primary
ArticleMol. Cell, Vol. 18, Issue 2, Page 149-59, Year 2005
TitleConservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
AuthorsMarc C Morais, Kyung H Choi, Jaya S Koti, Paul R Chipman, Dwight L Anderson, Michael G Rossmann
Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, Indiana 47907, USA.
KeywordsBacillus Phages (chemistry), Capsid (chemistry), Capsid Proteins (chemistry), Cryoelectron Microscopy, DNA, Viral (chemistry), Imaging, Three-Dimensional, Models, Molecular, Models, Structural, Protein Conformation, Protein Structure, Secondary, Protein Structure, Tertiary
LinksPII: S1097-2765(05)01183-4, DOI: 10.1016/j.molcel.2005.03.013, PubMed: 15837419
Components
ID 1 : Late protein Gp8
Image
DescriptionMajor head protein
Typepolypeptide(L)
Formula weight30656.020 Da
Number of molecules3
ID1
SourceMethod: Isolated from a genetically manipulated source
Gene: Phi29-like viruses, phi29, 8, ID:10756, Bacillus phage phi29
Host: Bacillus, ID:1423, Bacillus subtilis

LinksSequence view
Sample
Assembly
Aggregation statePARTICLE
NameFiberless isometric phi29 capsid
Entity assembly
Assembly-ID1
DetailsThe virus particle is a protein shell with icosahedral symmetry. To generate the complete icosahedral particle, apply the following 59 matrices to the three chains in the icosahedral asymmetric unit, and combine with the original coordinates of the icosahedral asymmetric unit:
NameThe capsid protein assembles a T=3 icosahedral virus shell.
Virus entity
Virus host categoryBacteria
Virus host growth cellBacillus subtilus
Virus host speciesBacillus subtilus
Virus typebacteriophage
Buffer
Nametris-HCL
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH7.8
Sample concentration1.0 mg/ml
Sample support
Detailselectron microscopy grid - in vitreous ice
Vitrification
Detailsfrozen in liquid ethane
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: FEI/PHILIPS CM200FEG/ST
Electron gun
Electron sourceField emmission gun
Accelerating voltage200 kV
Lens
MagnificationNominal: 38000 X
CsNominal: 2.0 mm
Specimen holder
Tilt angleMin: 0.0 degrees, Max: 0.0 degrees
Temperature100 Kelvin
Detector
TypeKODAK SO163 FILM
Processing
2D projection selection
Software nameSitus (colores)
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
CTF correction methodInverse of CTF was applied to images. Both phases and amplitudes were corrected.
DetailsSoftware used included P3DR (3D reconstructions), PFT (initial orientation improvement), and POR (final orientation refinement.
Method3D reconstructions were calculated using the Fourier-Bessel method. Initial orientations were found via common-lines, improved using model based polar Fourier transform methods, and finally refined by minimizing the vector difference between between structure factors calculated from a particle image and those from a central section of the Fourier transform of the model.
Nominal pixel size1.8421 A/pix
Resolution7.9 A
3D fitting
Method6D search for each symmetry related molecule in the icosahedral asymmetric unit
Refinement Protocolrigid body
Refinement SpaceREAL
Software nameSitus (colores)
Target criteriarigid body refinement in real space against laplacian filtered EM density, using the program COLORES in the package SITUS. Each molecule in the T=3 asymmetric unit was refined separately.
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms1080
Protein atoms1080
Download
PDB format
Allpdb1yxn.ent.gz
pdb1yxn.ent (uncompressed file)
Header onlypdb1yxn.ent.gz
mmCIF format
mmCIF1yxn.cif.gz
XML format
All1yxn.xml.gz
No-atom1yxn-noatom.xml.gz
Ext-atom1yxn-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 2.9 MB
.webm (WebM/VP8 format), 3.9 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 2.8 MB
.webm (WebM/VP8 format), 3.8 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.7 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.5 MB
movie #7
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 4.8 MB