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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, Image by UCSF CHIMERA

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

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

Supplemental images
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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, PMC: PMC4138882
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).
Applied SymmetryO (octahedral)
Download
Data from EMDB
Header (meta data in XML format)emd-5438.xml (7.3 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