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- EMDB-5288: The single particle reconstruction of the human Toll-like recepto... -

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Basic information

Entry
Database: EMDB / ID: 5288
TitleThe single particle reconstruction of the human Toll-like receptor 5 ectodomain in detergent
KeywordsToll-like receptor 5 / ectodomain
Sampletoll-like receptor 5 ectodomain
SourceHomo sapiens / human
Map dataThis is the volume of the hTLR5 ectodomain.
Methodsingle particle reconstruction, at 26 A resolution
AuthorsZhou K / Kanai R / Lee P / Wang HW / Modis Y
CitationJ. Struct. Biol., 2012, 177, 402-409

J. Struct. Biol., 2012, 177, 402-409 StrPapers
Toll-like receptor 5 forms asymmetric dimers in the absence of flagellin.
Kaifeng Zhou / Ryuta Kanai / Phong Lee / Hong-Wei Wang / Yorgo Modis

DateDeposition: May 2, 2011 / Header (metadata) release: May 5, 2011 / Map release: Dec 19, 2011 / Last update: May 2, 2011

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.57
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 3.57
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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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.

Voxel sizeX=Y=Z: 2.14 A
Density
Contour Level:3.57 (by author), 3.57 (movie #1):
Minimum - Maximum-5.61073 - 11.9316
Average (Standard dev.)9.24672e-10 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
CellA=B=C: 214 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-5.61111.9320.000

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Supplemental data

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Sample components

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Entire toll-like receptor 5 ectodomain

EntireName: toll-like receptor 5 ectodomain / Details: The sample was monodisperse / Number of components: 2 / Oligomeric State: dimer
MassTheoretical: 200 kDa / Experimental: 200 kDa / Measured by: gel filtration

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Component #1: protein, Toll-like receptor

ProteinName: Toll-like receptor / a.k.a: TLR5 / Oligomeric Details: dimer / Recombinant expression: Yes / Number of Copies: 2
MassTheoretical: 200 kDa / Experimental: 200 kDa
SourceSpecies: Homo sapiens / human
Source (engineered)Expression System: Sf9 insect cells / Vector: pAcGP67-A
Source (natural)Organelle: membrane / Location in cell: plasma membrane / Cell: Sf9 insect cells
External referencesInterPro: InterPro: 017241

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.005 mg/ml / Buffer solution: 10 mM TEA, 0.15 M NaCl / pH: 7.5
Support filmthin carbon covered home-made holey carbon on 400 mesh copper grid
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.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Aug 1, 2010
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM
LensMagnification: 52000 X (nominal), 52000 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 1200 nm
Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 50

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Image processing

ProcessingMethod: single particle reconstruction / Number of class averages: 100 / Number of projections: 3087 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Random conical tilt followed by projection matching refinement
Software: IMAGIC SPIDER
Details: Final maps were calculated from all the particles by back-projection reconstruction.
Resolution: 26 A / Resolution method: FSC 0.5

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