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Helical reconstruction of the bacterial L-type flagella filament

by helical reconstruction, at 4 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 550, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 550, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1641
TitleHelical reconstruction of the bacterial L-type flagella filament
MapThis is a cryo-EM map of L-type flagellin including data up to 4 Angstrom resolution.
SampleS. enterica serovar Typhimurium L-type flagella filament
Keywordsbacterial flagellum
AuthorsMaki-Yonekura S, Yonekura K, Namba K
DateDeposition: 2009-08-12, Header release: 2010-01-26, Map release: 2011-08-19, Last update: 2012-10-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 550, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 550, Image by UCSF CHIMERA

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

PDB-3a5x

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleNat. Struct. Mol. Biol., Vol. 17, Issue 4, Page 417-22, Year 2010
TitleConformational change of flagellin for polymorphic supercoiling of the flagellar filament.
AuthorsSaori Maki-Yonekura, Koji Yonekura, Keiichi Namba
Dynamic NanoMachine Project, International Cooperative Research Project, Japan Science and Technology Agency, Suita, Osaka, Japan.
KeywordsBacterial Physiological Phenomena, Flagella (chemistry), Flagellin (chemistry, 12777-81-0), Protein Conformation
LinksDOI: 10.1038/nsmb.1774, PubMed: 20228803
Map
Fileemd_1641.map.gz ( map file in CCP4 format, 33525 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
251 pix
1 A/pix
= 251. A
131 pix
1 A/pix
= 261. A
261 pix
1 A/pix
= 131. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:550 (by author), 550 (movie #1):
Minimum - Maximum: -948.453 - 2134.49
Average (Standard dev.): 4.55795 (60.6009)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions131261251
Origin000
Limit130260250
Spacing131261251
Unit CellA: 131 A, B: 261 A, C: 251 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z111
M x/y/z131261251
origin x/y/z0.0000.0000.000
length x/y/z131.000261.000251.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS261131251
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-948.4532134.4914.558
Annotation DetailsThis is a cryo-EM map of L-type flagellin including data up to 4 Angstrom resolution.
Supplement
Images
Images
Sample
NameS. enterica serovar Typhimurium L-type flagella filament
Number of Components1
Component #1: protein - Flagella filament
Scientific nameFlagella filament
Oligomeric DetailsHelical assembly
Scientific Name of SpeciesSalmonella enterica subsp. enterica serovar Typhimurium
Common Name of SpeciesSalmonella enterica subsp. enterica serovar Typhimurium
NCBI taxonomy90371
StrainSJW1660
Recombinant expressionNo
Natural SourceCell Location: Outside cell
Experiment
Sample Preparation
Helical ParametersHand: LEFT HANDED
Specimen Statefilament
Vitrification
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeJEOL 3000SFF
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Illumination ModeFLOOD BEAM
Lens
Imaging ModeBRIGHT FIELD
Specimen Holder
HolderTop entry
ModelJEOL
Temperature4 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerOTHER
Sampling Size5
Processing
Methodhelical reconstruction
3D reconstruction
AlgorithmHelical reconstruction
SoftwareHandmade
CTF CorrectionEach filament
Resolution By Author4 A
Resolution MethodFigure of merit
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1641.xml (6.1 KB)
Map dataemd_1641.map.gz (454.8 KB)
Imagesem-1641.png (170.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1641
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5 MB
Session file for UCSF-Chimera, 26.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.8 KB