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Structure of tetrameric MotA complex

by single particle reconstruction, at 25 A resolution

Movie

Orientation:

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

#2: Surface view colored by radius, Surface level: 1, Imaged by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 3417
TitleStructure of tetrameric MotA complex
MapReconstruction of Aquifex aeolicus stator protein, tetrameric MotA complex
SampleAquifex aeolicus MotA
KeywordsFlagella motor, Stator, Single Particle analysis, Proton motive force
AuthorsTakekawa N, Terahara N, Kato T, Gohara M, Mayanagi K, Hijikata A, Onoue Y, Kojima S, Shirai T, Namba K, Homma M
DateDeposition: 2016-04-27, Header release: 2016-05-18, Map release: 2017-08-02, Last update: 2017-08-02
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

#2: Surface view colored by radius, Surface level: 1, Imaged by UCSF CHIMERA

Supplemental images
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Article
Citation - Primary
ArticleSci Rep, Vol. 6, Page 31526-31526, Year 2016
TitleThe tetrameric MotA complex as the core of the flagellar motor stator from hyperthermophilic bacterium.
AuthorsNorihiro Takekawa, Naoya Terahara, Takayuki Kato, Mizuki Gohara, Kouta Mayanagi, Atsushi Hijikata, Yasuhiro Onoue, Seiji Kojima, Tsuyoshi Shirai, Keiichi Namba, Michio Homma
Division of Biological Science, Graduate School of Science, Nagoya University, Chikusa-ku, Nagoya 464-8602, Japan.
Graduate School of Frontier Biosciences, Osaka University, 1-3 Yamadaoka, Suita, Osaka 565-0871, Japan.
Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8581, Japan.
JST, PRESTO, Fukuoka 812-8582, Japan.
Department of Bioscience, Nagahama Institute of BioScience and Technology, 1266 Tamura, Nagahama, 526-0829, Japan.
LinksPubMed: 27531865, DOI: 10.1038/srep31526, PMC: PMC4987623
Map
Fileemd_3417.map.gz ( map file in CCP4 format, 1025 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
2.8 A/pix
= 179.2 A
64 pix
2.8 A/pix
= 179.2 A
64 pix
2.8 A/pix
= 179.2 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum: -3.35296297 - 3.4676733
Average (Standard dev.): 0.01830916 (0.3995882)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin-32-32-32
Limit313131
Spacing646464
Unit CellA= B= C: 179.2 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.8 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.82.82.8
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z179.200179.200179.200
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3.3533.4680.018
Annotation DetailsReconstruction of Aquifex aeolicus stator protein, tetrameric MotA complex
Supplement
Images
Images
Sample
NameAquifex aeolicus MotA
Number of Components1
Oligomeric Statetetramer
Theoretical Mass0.109MDa
Component #1: protein - Chemotaxis protein MotA
Scientific nameMotility protein A
Common NameChemotaxis protein MotA
Theoretical Mass0.109 MDa
Oligomeric DetailsTetramer
Number of Copies4
Scientific Name of SpeciesAquifex aeolicus
NCBI taxonomy63363
StrainVF5
Recombinant expressionYes
Engineered SourceVector: pColdI
NCBI taxonomy: 562
Expression system: Escherichia coli
Exp System Strain: BL21-CodonPlus(DE3)-RIPL
LinksUni Prot: O67122
Experiment
Sample Preparation
Staining2% w/v uranyl acetate
Specimen Stateparticle
Specimen Conc0.1 mg/ml
Specimen Support Details200 mesh copper grid with continuous carbon suport, glow discharged
BufferDetails: 50 mM Tris-HCl, 200 mM NaCl, 0.02% DMNG
pH: 8
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeJEOL 3200FSC
Date16-NOV-2015
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose2.8 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 80000, Calibrated: 107140
Nominal Cs4.1 mm
Imaging ModeBRIGHT FIELD
Defocus1135 nm - 2200 nm
Energy FilterEnergy Filter: Omega Filter , Energy Window: 0-20 eV
Specimen Holder
HolderNitrogen cooled
ModelJEOL 3200FSC CRYOHOLDER
Temperature85.5 K ( 85.5 - 85.7 K)
Camera
DetectorTVIPS TEMCAM-F415 (4k x 4k)
Image Acquisition
#1
Number of Digital Images50
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareRelion-1.4
Resolution By Author25 A
Resolution MethodFSC 0.143
Single Particle
Applied SymmetryC2 (2 fold cyclic)
Number of Projections5419
Download
Data from EMDB
Header (meta data in XML format)emd-3417.xml (7.5 KB)
Map dataemd_3417.map.gz (741.5 KB)
Imagesemd_3417.png (327.4 KB)
emd_3417_1.png (319.5 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-3417
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.9 KB