PDB-1yxn: Pseudo-atomic model of a fiberless isometric variant of...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1yxn
Title	Pseudo-atomic model of a fiberless isometric variant of bacteriophage phi29
Descriptor	Major head protein
Keywords	Virus, phi29, capsid, icosahedral virus capsid, hk97 fold, phage, bacterial immuno-globulin, BIG2, Icosahedral virus
Authors	Morais, M.C., Choi, K.H., Koti, J.S., Chipman, P.R., Anderson, D.L., Rossmann, M.G.
Date	Deposition: 2005-02-22, Release: 2005-04-26
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie 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 viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-1116 CiteFit EMDB-1120 CiteFit EMDB-1117 Cite PDB-1f00 PDB-1ohg Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram EMDB-5504 PDB-3izg PDB-1if0 PDB-2xyy List of similar structure data about Omokage system

Article
Citation - primary
Article	Mol. Cell, Vol. 18, Issue 2, Page 149-59, Year 2005
Title	Conservation of the capsid structure in tailed dsDNA bacteriophages: the pseudoatomic structure of phi29.
Authors	Marc 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.
Keywords	Bacillus 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
Links	PII: S1097-2765(05)01183-4, DOI: 10.1016/j.molcel.2005.03.013, PubMed: 15837419

Components
ID 1 : Late protein Gp8
Image
Description	Major head protein
Type	polymer
Formula weight	30656.020 Da
Number of molecules	3
Source	Method: Isolated from a genetically manipulated source Gene: Phi29-like viruses, phi29, 8, ID:10756, Bacillus phage phi29 Host: Bacillus, ID:1423, Bacillus subtilis
Links	Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	Fiberless isometric phi29 capsid
Entity assembly
Details	The 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:
Name	The capsid protein assembles a T=3 icosahedral virus shell.
Virus entity
Virus host category	Bacteria
Virus host growth cell	Bacillus subtilus
Virus host species	Bacillus subtilus
Virus type	bacteriophage
Buffer
Name	tris-HCL
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.8
Sample concentration	1.0 mg/ml
Sample support
Details	electron microscopy grid - in vitreous ice
Vitrification
Details	frozen in liquid ethane

Processing
2D projection selection
Software name	Situs (colores)
Single particle entity
Symmetry type	ICOSAHEDRAL
3D reconstruction
CTF correction method	Inverse of CTF was applied to images. Both phases and amplitudes were corrected.
Details	Software used included P3DR (3D reconstructions), PFT (initial orientation improvement), and POR (final orientation refinement.
Method	3D 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 size	1.8421 A/pix
Resolution	7.9 A
3D fitting
Method	6D search for each symmetry related molecule in the icosahedral asymmetric unit
Refinement Protocol	rigid body
Refinement Space	REAL
Software name	Situs (colores)
Target criteria	rigid 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
Total atoms	1080
Protein atoms	1080

PDB format

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Header only

mmCIF format

mmCIF

XML format

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No-atom

Ext-atom

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