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3D reconstruction of a self-assembling designed oligomer with octahedral symmetry

by single particle reconstruction, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.8, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.8, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5438
Title3D reconstruction of a self-assembling designed oligomer with octahedral symmetry
MapReconstruction of designed self-assembling protein oligomer with octahedral symmetry
SampleDesigned protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Keywordsoctahedral symmetry, designed
AuthorsVollmar BS, King NP, Baker D, Gonen T
DateDeposition: 2012-06-24, Header release: 2012-06-29, Map release: 2012-06-29, Last update: 2012-12-19
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 1.8, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 1.8, 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
ArticleScience, Vol. 336, Issue 6085, Page 1171-4, Year 2012
TitleComputational design of self-assembling protein nanomaterials with atomic level accuracy.
AuthorsNeil P King, William Sheffler, Michael R Sawaya, Breanna S Vollmar, John P Sumida, Ingemar André, Tamir Gonen, Todd O Yeates, David Baker
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
KeywordsChromatography, Gel, Cloning, Molecular, Computational Biology, Computer Simulation, Crystallography, X-Ray, Escherichia coli (genetics), Hydrogen Bonding, Microscopy, Electron, Models, Molecular, Molecular Weight, Mutation, Nanostructures, Protein Engineering, Protein Multimerization, Protein Structure, Secondary, Protein Subunits (chemistry), Proteins (chemistry)
LinksDOI: 10.1126/science.1219364, PubMed: 22654060
Map
Fileemd_5438.map.gz ( map file in CCP4 format, 6751 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
120 pix
1.474 A/pix
= 176.88 A
120 pix
1.474 A/pix
= 176.88 A
120 pix
1.474 A/pix
= 176.88 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1.8 (by author), 1.8 (movie #1):
Minimum - Maximum: -2.47524214 - 4.30226564
Average (Standard dev.): -2E-8 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions120120120
Origin000
Limit119119119
Spacing120120120
Unit CellA= B= C: 176.88 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.474 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.4741.4741.474
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z176.880176.880176.880
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS120120120
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-2.4754.302-0.000
Annotation DetailsReconstruction of designed self-assembling protein oligomer with octahedral symmetry
Supplement
Images
Images
Sample
NameDesigned protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Number of Components1
Oligomeric State24
Theoretical Mass0.48MDa
DetailsMonodisperse sample
Component #1: protein - Propanediol utilization polyhedral body protein PduT
Scientific namePropanediol utilization polyhedral body protein PduT
DetailsMutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Number of Copies24
Scientific Name of SpeciesSalmonella enterica
NCBI taxonomy28901
Recombinant expressionYes
Engineered SourceVector: pET29b
NCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Conc0.3 mg/ml
Specimen Support DetailsQuantifoil R1.2/1.3 holey carbon 400 mesh copper grids
Specimen Stateparticle
BufferDetails: 25 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT
pH: 8
Vitrification
MethodBlotted with filter paper and plunged into liquid ethane.
Cryogen NameETHANE
Humidity100
InstrumentFEI VITROBOT MARK III
Imaging
MicroscopeFEI TECNAI F20
Date12-JUL-2011
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 100000, Calibrated: 217096
Nominal Cs2.12 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 2000 nm
Specimen Holder
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Camera
DetectorTVIPS TEMCAM-F816 (8k x 8k)
Image Acquisition
Number of Digital Images565
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareFREALIGN
CTF CorrectionCTFFIND3
DetailsReconstruction was calculated based on 2x binned images yielding a pixel size of 1.474 A/pixel.
Resolution By Author20 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections42025
DetailsParticles were selected using the automatic selection program Electron Micrograph Utility (cryoem.ucsf.edu).
Download
Data from EMDB
Header (meta data in XML format)emd-5438.xml (7.2 KB)
Map dataemd_5438.map.gz (2.2 MB)
Imagesemd_5438_1.jpg (49.5 KB)
emd_5438_2.tif (178.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5438
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 26.4 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 26.5 KB