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Structrue of truncated portal(portal602) complex with gp4 from bacteriophage P22

by single particle reconstruction, at 8.5 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3.850629391, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 3.850629391, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1482
TitleStructrue of truncated portal(portal602) complex with gp4 from bacteriophage P22
Mapmap of portal602 complex with gp4
Sampletruncated portal complex with gp4 from bacteriophage P22
AuthorsZheng H, Olia AS, Gonen M, Andrews S, Cingolani G, Gonen T
DateDeposition: 2008-02-26, Header release: 2008-02-26, Map release: 2009-03-31, Last update: 2013-12-25
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3.850629391, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 3.850629391, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleMol. Cell, Vol. 29, Issue 3, Page 376-83, Year 2008
TitleA conformational switch in bacteriophage p22 portal protein primes genome injection.
AuthorsHongjin Zheng, Adam S Olia, Melissa Gonen, Simeon Andrews, Gino Cingolani, Tamir Gonen
Department of Biochemistry, University of Washington, 1705 NE Pacific Street, Seattle, WA 98195, USA.
KeywordsBacteriophage P22 (chemistry), Binding Sites, Capsid Proteins (chemistry), DNA, Viral (chemistry), Genome, Models, Molecular, Protein Binding, Protein Conformation, Viral Tail Proteins (chemistry), portal protein, bacteriophage P22
LinksPII: S1097-2765(08)00006-3, DOI: 10.1016/j.molcel.2007.11.034, PubMed: 18280242, PMC: PMC3936403
Map
Fileemd_1482.map.gz ( map file in CCP4 format, 6751 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
2.48 A/pix
= 297.6 A
120 pix
2.48 A/pix
= 297.6 A
120 pix
2.48 A/pix
= 297.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2.75, 3.8506294 (movie #1):
Minimum - Maximum: -2.59705 - 7.69801
Average (Standard dev.): -7.13014e-09 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions120120120
Origin-60-60-60
Limit595959
Spacing120120120
Unit CellA= B= C: 297.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.48 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.482.482.48
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z297.600297.600297.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-2.5977.698-0.000
Annotation Detailsmap of portal602 complex with gp4
Supplement
Images
Images
Sample
Nametruncated portal complex with gp4 from bacteriophage P22
Number of Components2
Oligomeric State12mer of portal with 12mer of gp4
Component #1: protein - gp1, gp4
Scientific namegp1, gp4
Scientific Name of SpeciesEnterobacteria phage P22
NCBI taxonomy10754
Recombinant expressionYes
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeOTHER
Lens
Imaging ModeOTHER
Specimen Holder
HolderEucentric
ModelOTHER
Camera
Processing
Methodsingle particle reconstruction
3D reconstruction
Resolution By Author8.5 A
Resolution MethodFSC 0.143
Download
Data from EMDB
Header (meta data in XML format)emd-1482.xml (5.2 KB)
Map dataemd_1482.map.gz (5.5 MB)
Images1482.gif (26.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1482
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 19.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 19.6 KB