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- EMDB-9859: Structure of the archaeal Archaeoglobus fulgidus oligosaccharyltr... -

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Basic information

Entry
Database: EMDB / ID: EMD-9859
TitleStructure of the archaeal Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol
Map data
Sample
  • Complex: Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol
Biological speciesArchaeoglobus fulgidus (archaea)
Methodsingle particle reconstruction / negative staining / Resolution: 21.0 Å
AuthorsKawasaki Y / Mayanagi K / Kohda D
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP26119002 Japan
CitationJournal: To Be Published
Title: Structure of the archaeal Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol
Authors: Kawasaki Y / Mayanagi K / Kohda D
History
DepositionMar 20, 2019-
Header (metadata) releaseMar 25, 2020-
Map releaseMar 25, 2020-
UpdateMar 25, 2020-
Current statusMar 25, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.66
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.66
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9859.png

Downloads & links

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Map

FileDownload / File: emd_9859.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 80 pix.
= 220.8 Å		2.76 Å/pix.
x 80 pix.
= 220.8 Å		2.76 Å/pix.
x 80 pix.
= 220.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.66 / Movie #1: 2.66
Minimum - Maximum-3.7689376 - 9.383638
Average (Standard dev.)-0.00000000130 (±1.0000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-14-14-14
Dimensions808080
Spacing808080
CellA=B=C: 220.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z220.800220.800220.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-14-14-14
NC/NR/NS808080
D min/max/mean-3.7699.384-0.000

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Supplemental data

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Sample components

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Entire : Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapp...

EntireName: Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol
Components
  • Complex: Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol

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Supramolecule #1: Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapp...

SupramoleculeName: Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) trapped in amphipol
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Archaeoglobus fulgidus (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC4H11NO3Tris-HCl
100.0 mMNaClsodium chloride

Details: 20 mM Tris-HCl (pH 7.4), 100 mM NaCl
StainingType: NEGATIVE / Material: uranyl acetate
Details: Negatively stained EM specimens were prepared using uranyl-acetate stain.
GridModel: Homemade / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
DetailsThe sample was monodisperse

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: FEI EAGLE (2k x 2k) / Digitization - Dimensions - Width: 2048 pixel / Digitization - Dimensions - Height: 2048 pixel / Number grids imaged: 1 / Number real images: 170 / Average exposure time: 120.0 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm

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Image processing

Particle selectionNumber selected: 11122
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN (ver. 1.9) / Software - details: EMAN refine command was used. / Number images used: 11122
Initial angle assignmentType: COMMON LINE / Software - Name: EMAN (ver. 1.9) / Software - details: EMAN StartAny command was used.
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Number reference projections: 180
Software - Name: EMAN (ver. 1.9) / Software - details: EMAN refine command was used.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3wak


Chain - Chain ID: A / Chain - Residue range: 5-868
DetailsFitting was done using Chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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