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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
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