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The single particle reconstruction of the human Toll-like receptor 5 ectodomain in detergent

by single particle reconstruction, at 26 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3.57, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3.57, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5288
TitleThe single particle reconstruction of the human Toll-like receptor 5 ectodomain in detergent
MapThis is the volume of the hTLR5 ectodomain.
Sampletoll-like receptor 5 ectodomain
KeywordsToll-like receptor 5, ectodomain
AuthorsZhou K, Kanai R, Lee P, Wang HW, Modis Y
DateDeposition: 2011-05-02, Header release: 2011-05-05, Map release: 2011-12-19, Last update: 2011-12-19
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3.57, Image by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3.57, Image by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
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Article
Citation - Primary
ArticleJ. Struct. Biol., Vol. 177, Issue 2, Page 402-9, Year 2012
TitleToll-like receptor 5 forms asymmetric dimers in the absence of flagellin.
AuthorsKaifeng Zhou, Ryuta Kanai, Phong Lee, Hong-Wei Wang, Yorgo Modis
Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA.
KeywordsFlagellin (chemistry, 12777-81-0), Glycosylation, Humans, Models, Molecular, Particle Size, Protein Binding, Protein Interaction Domains and Motifs, Protein Multimerization, Protein Processing, Post-Translational, Protein Structure, Quaternary, Structural Homology, Protein, Surface Properties, TLR5 protein, human, Toll-Like Receptor 5 (chemistry)
LinksPII: S1047-8477(11)00348-0, DOI: 10.1016/j.jsb.2011.12.002, PubMed: 22173220
Map
Fileemd_5288.map.gz ( map file in CCP4 format, 3908 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
2.14 A/pix
= 214. A
100 pix
2.14 A/pix
= 214. A
100 pix
2.14 A/pix
= 214. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:3.57 (by author), 3.57 (movie #1):
Minimum - Maximum: -5.61073 - 11.9316
Average (Standard dev.): 9.24672e-10 (1)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
Unit CellA= B= C: 214 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.14 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.142.142.14
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z214.000214.000214.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-5.61111.9320.000
Annotation DetailsThis is the volume of the hTLR5 ectodomain.
Supplement
Images
Images
Sample
Nametoll-like receptor 5 ectodomain
Number of Components2
Oligomeric Statedimer
Theoretical Mass0.2MDa
DetailsThe sample was monodisperse
Mass-estimation Methodgel filtration
Experimental Mass0.2MDa
Component #1: protein - TLR5
Scientific nameToll-like receptor
Common NameTLR5
Theoretical Mass0.2 MDa
Experimental Mass0.2 MDa
Oligomeric Detailsdimer
Number of Copies2
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionYes
Natural SourceCell: Sf9 insect cells
Organelle: membrane
Cell Location: plasma membrane
Engineered SourceVector: pAcGP67-A
Expression system: Sf9 insect cells
LinksInter Pro: IPR:017241
Experiment
Sample Preparation
StainingThe protein solution was applied onto a thin-carbon-covered holey carbon copper grid and negatively stained in 1% uranyl-formate solution for 1 minute.
Specimen Conc0.005 mg/ml
Specimen Support Detailsthin carbon covered home-made holey carbon on 400 mesh copper grid
Specimen Stateparticle
BufferDetails: 10 mM TEA, 0.15 M NaCl
pH: 7.5
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Date01-AUG-2010
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 52000, Calibrated: 52000
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 1200 nm
Specimen Holder
HolderEucentric
ModelSIDE ENTRY, EUCENTRIC
Camera
DetectorGATAN ULTRASCAN 4000 (4k x 4k)
Image Acquisition
#1
Number of Digital Images50
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmRandom conical tilt followed by projection matching refinement
SoftwareIMAGIC SPIDER
DetailsFinal maps were calculated from all the particles by back-projection reconstruction.
Resolution By Author26 A
Resolution MethodFSC 0.5
Single Particle
Number of Class Averages100
Number of Projections3087
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-5288.xml (7.4 KB)
Map dataemd_5288.map.gz (3.4 MB)
Imagesemd_5288_1.png (300.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5288
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.2 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, 26.7 KB