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Homology model of avian polyomavirus asymmetric unit

by single particle (icosahedral) reconstruction, at 11.3 A resolution

Movie

Orientation:

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

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

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

#4: Depositted structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-5180, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-5180, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 3iys
TitleHomology model of avian polyomavirus asymmetric unit
DescriptorMajor capsid protein VP1
KeywordsVIRUS, avian, polyomavirus, APV, icosahedral virus
AuthorsShen, P.S., Enderlein, D., Nelson, C.D.S., Carter, W.S., Kawano, M., Xing, L., Swenson, R.D., Olson, N.H., Baker, T.S., Cheng, R.H., Atwood, W.J., Johne, R., Belnap, D.M.
DateDeposition: 2010-04-19, Release: 2011-01-26
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, Image by Jmol

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

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

#4: Depositted structure unit, Image by Jmol

#5: Superimposing with simplified surface model of EM map, EMDB-5180, Image by Jmol

#6: Superimposing with EM 3D map: EMDB-5180, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
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EMDB-5180

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Article
Citation - primary
ArticleVirology, Vol. 411, Issue 1, Page 142-52, Year 2011
TitleThe structure of avian polyomavirus reveals variably sized capsids, non-conserved inter-capsomere interactions, and a possible location of the minor capsid protein VP4.
AuthorsPeter S Shen, Dirk Enderlein, Christian D S Nelson, Weston S Carter, Masaaki Kawano, Li Xing, Robert D Swenson, Norman H Olson, Timothy S Baker, R Holland Cheng, Walter J Atwood, Reimar Johne, David M Belnap
Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602, USA.
KeywordsAnimals, Capsid (ultrastructure), Capsid Proteins (metabolism), Cryoelectron Microscopy, Macromolecular Substances (ultrastructure), Melopsittacus (virology), Polyomavirus (isolation & purification)
LinksDOI: 10.1016/j.virol.2010.12.005, PubMed: 21239031, PMC: PMC3057058
Components
ID 1 : Major structural protein VP1
Image
DescriptionMajor capsid protein VP1
Typepolypeptide(L)
Formula weight37449.703 Da
Number of molecules6
ID1
SourceMethod: Isolated from a natural source
Common name: BFPyV
NCBI taxonomy: ID:10625
Organism scientific: Budgerigar fledgling disease polyomavirus
LinksUniProt: P13891, Sequence view
Sample
Assembly
Aggregation statePARTICLE
DetailsCryo-EM single particle reconstruction
Nameavian polyomavirus
Entity assembly
Assembly-ID1
Virus entity
Virus host categoryvertebrates
Virus host speciesavian
Virus isolateSPECIES
Virus typevirion
Buffer
NameGP buffer with 250 mM L-arginine
Experiment
Reconstruction methodSINGLE PARTICLE
Specimen typeVITREOUS ICE (CRYO EM)
Sample preparation
pH10.7
Sample support
Detailsavian polyomavirus in holey carbon grid
Vitrification
Cryogen nameETHANE
DetailsAPV
Humidity100%
InstrumentFEI vitrobot
Method3 second blot
Temp4.0 Kelvin
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
Date23-APR-2007
Electron gun
Accelerating voltage200 kV
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 39000 X, Nominal: 39000 X
Astigmatismastigmatism was corrected at 59,000 times magnification
Detector distance0.0
Nominal defocusMax: 4900 nm, Min: 500 nm
Specimen holder
Specimen holderModel: GATAN LIQUID NITROGEN, Type: Side entry liquid nitrogen-cooled cryo specimen holder
Tilt angleMin: 0.0 degrees, Max: 0.0 degrees
Temperature90 Kelvin
Recording temperatureMaximum: 95, Minimum: 88
Processing
2D projection selection
Software nameUCSF Chimera
Single particle entity
Symmetry typeICOSAHEDRAL
3D reconstruction
Actual pixel size1.57 A/pix
CTF correction methodfull CTF correction (FSC cutoff 0.3)
Magnification calibrationagainst simian virus 40 atomic coordinates
MethodFourier Bessel
Nominal pixel size1.63 A/pix
Number of particles5338
Resolution11.3 A
SoftwarePFT3DR
3D fitting
Methodrigid body
Refinement Protocolrigid body
Refinement SpaceREAL
Software nameUCSF Chimera
Target criteriacross-correlation coefficient
3D fitting list
3D Fitting ID1
PDB entry ID1SIE
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
Total atoms2004
Protein atoms2004
Download
PDB format
Allpdb3iys.ent.gz
pdb3iys.ent (uncompressed file)
Header onlypdb3iys.ent.gz
mmCIF format
mmCIF3iys.cif.gz
XML format
All3iys.xml.gz
No-atom3iys-noatom.xml.gz
Ext-atom3iys-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.3 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.2 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 2.7 MB
.webm (WebM/VP8 format), 3.6 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.9 MB
.webm (WebM/VP8 format), 5.7 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.8 MB