[English] 日本語
Yorodumi
- EMDB-9858: Structure of the archaeal Archaeoglobus fulgidus oligosaccharyltr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9858
TitleStructure of the archaeal Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) embedded in nanodisc
Map data
Sample
  • Complex: Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) embedded in nanodisc
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) embedded in nanodisc
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

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 2.7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9858.png

Downloads & links

-
Map

FileDownload / File: emd_9858.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: 2.7 / Movie #1: 2.7
Minimum - Maximum-3.5697725 - 8.499276
Average (Standard dev.)-0.00000000152 (±1)
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-3.5708.499-0.000

-
Supplemental data

-
Sample components

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

EntireName: Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) embedded in nanodisc
Components
  • Complex: Archaeoglobus fulgidus oligosaccharyltransferase (AfAglB-L) embedded in nanodisc

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

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

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
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
DetailsThis sample was monodisperse

-
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: 250 / 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

+
Image processing

Particle selectionNumber selected: 43985
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: 43985
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)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more