EMDB-5438: 3D reconstruction of a self-assembling designed oligom...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5438
Title	3D reconstruction of a self-assembling designed oligomer with octahedral symmetry
Map	Reconstruction of designed self-assembling protein oligomer with octahedral symmetry
Sample	Designed 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
Keywords	octahedral symmetry, designed
Authors	Vollmar BS, King NP, Baker D, Gonen T
Date	Deposition: 2012-06-24, Header release: 2012-06-29, Map release: 2012-06-29, Last update: 2012-12-19
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie 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	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-3vcd Cite PDB-4dcl Cite PDB-4ddf Cite PDB-4egg Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-2865 EMDB-1295 PDB-2ygd List of similar structure data about Omokage system

Article
Citation - Primary
Article	Science, Vol. 336, Issue 6085, Page 1171-4, Year 2012
Title	Computational design of self-assembling protein nanomaterials with atomic level accuracy.
Authors	Neil 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.
Keywords	Chromatography, 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)
Links	DOI: 10.1126/science.1219364, PubMed: 22654060

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 176.88 A , B = 176.88 A , C = 176.88 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 1.474 A , Y = 1.474 A , Z = 1.474 A

CCP4 map header info

Annotation Details

Reconstruction of designed self-assembling protein oligomer with octahedral symmetry

Sample
Name	Designed 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 Components	1
Oligomeric State	24
Theoretical Mass	0.48 MDa
Details	Monodisperse sample
Component #1: protein - Propanediol utilization polyhedral body protein PduT
Scientific name	Propanediol utilization polyhedral body protein PduT
Details	Mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
Number of Copies	24
Scientific Name of Species	Salmonella enterica (NCBI Taxonomy: 28901)
Recombinant expression	Yes
Engineered Source	Vector: pET29b Exp System: Escherichia coli (NCBI Taxonomy: 562)

Experiment
Sample Preparation
Specimen Conc	0.3 mg/ml
Specimen Support Details	Quantifoil R1.2/1.3 holey carbon 400 mesh copper grids
Specimen State	particle
Buffer	Details: 25 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT pH: 8
Vitrification
Method	Blotted with filter paper and plunged into liquid ethane.
Cryogen Name	ETHANE
Humidity	100
Instrument	FEI VITROBOT MARK III
Imaging
Microscope	FEI TECNAI F20
Date	12-JUL-2011
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Illumination Mode	SPOT SCAN
Lens
Magnification	Nominal: 100000 X, Calibrated: 217096 X
Nominal Cs	2.12 mm
Imaging Mode	BRIGHT FIELD
Defocus	1000 nm - 2000 nm
Specimen Holder
Holder	( GATAN LIQUID NITROGEN )
Tilt Angle	0 degrees - 0 degrees
Camera
Detector	8k x 8k TVIPS F816
Image Acquisition
Number of Digital Images	565

Processing
Method	single particle reconstruction
3 D reconstruction
Software	FREALIGN
CTF Correction	CTFFIND3
Details	Reconstruction was calculated based on 2x binned images yielding a pixel size of 1.474 A/pixel.
Resolution By Author	20
Resolution Method	FSC at 0.5 cutoff
Single Particle
Number of Projections	42025
Details	Particles were selected using the automatic selection program Electron Micrograph Utility (cryoem.ucsf.edu).

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

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