[English] 日本語
Yorodumi
- EMDB-26791: Cryo-EM subtomogram average of IFT-A in anterograde IFT trains at... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26791
TitleCryo-EM subtomogram average of IFT-A in anterograde IFT trains at 23 Angstrom resolution (Chlamydomonas reinhardtii)
Map dataPrimary masked map
Sample
  • Complex: IFT-A complex comprised of IFT43, IFT121, IFT122, IFT139, IFT140, and IFT144
Biological speciesChlamydomonas reinhardtii (plant)
Methodsubtomogram averaging / cryo EM / Resolution: 23.0 Å
AuthorsJordan MA / Pigino G
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Biorxiv / Year: 2022
Title: Integrative modeling reveals the molecular architecture of the Intraflagellar Transport A (IFT-A) complex
Authors: McCafferty CL / Papoulas O / Jordan MA / Hoogerbrugge G / Nichols C / Pigino G / Taylor DW / Wallingford JB / Marcotte EM
History
DepositionApr 27, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26791.png

Downloads & links

-
Map

FileDownload / File: emd_26791.map.gz / Format: CCP4 / Size: 2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPrimary masked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.07 Å/pix.
x 80 pix.
= 565.28 Å		7.07 Å/pix.
x 80 pix.
= 565.28 Å		7.07 Å/pix.
x 80 pix.
= 565.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.066 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.15
Minimum - Maximum-3.0948513 - 5.6137547
Average (Standard dev.)0.009711553 (±0.24373692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin110110110
Dimensions808080
Spacing808080
CellA=B=C: 565.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Composite polymer map

Fileemd_26791_additional_1.map
AnnotationComposite polymer map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Large 300px raw map

Fileemd_26791_additional_2.map
AnnotationLarge 300px raw map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : IFT-A complex comprised of IFT43, IFT121, IFT122, IFT139, IFT140,...

EntireName: IFT-A complex comprised of IFT43, IFT121, IFT122, IFT139, IFT140, and IFT144
Components
  • Complex: IFT-A complex comprised of IFT43, IFT121, IFT122, IFT139, IFT140, and IFT144

-
Supramolecule #1: IFT-A complex comprised of IFT43, IFT121, IFT122, IFT139, IFT140,...

SupramoleculeName: IFT-A complex comprised of IFT43, IFT121, IFT122, IFT139, IFT140, and IFT144
type: complex / Chimera: Yes / ID: 1 / Parent: 0
Details: Cryo-ET subtomogram averaging of an IFT-A complex, as observed in situ in the context of an anterograde intraflagellar transport (IFT) train in intact Chlamydomonas flagella
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: cilia

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7.2
GridModel: Quantifoil R3.5/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 291.15 K / Instrument: LEICA EM GP
DetailsFresh liquid cell cultures of 300 mL were grown for three to four days in TAP (Tris-acetate-phosphate) medium at 22 degrees C under a light-dark cycle with constant aeration. 3 microL undiluted Chlamydomonas cells were applied to the grid and mixed with 1 microL 10 nm colloidal gold particles (BBI solutions)

-
Electron microscopy

MicroscopeFEI TITAN
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Details: Images were recorded with an energy filter (GIF, Gatan image filter). Digital Micrograph software (Gatan) was used to tune the GIF, and SerialEM software was employed for the automated ...Details: Images were recorded with an energy filter (GIF, Gatan image filter). Digital Micrograph software (Gatan) was used to tune the GIF, and SerialEM software was employed for the automated acquisition of tomographic tilt series in low-dose mode.
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-10 / Number grids imaged: 34 / Average exposure time: 2.0 sec. / Average electron dose: 1.85 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 3.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

-
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 23.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PEET / Number subtomograms used: 9350
ExtractionNumber tomograms: 96 / Number images used: 9350 / Method: manual picking / Software - Name: IMOD
Details: bin6 tomograms were filtered with NAD (non-linear anisotropic diffusion) in IMOD to increase contrast and facilitate particle picking
CTF correctionSoftware - Name: IMOD
Details: CTF curves were estimated with CTFPLOTTER and the data were corrected by phase-flipping with CTFPHASEFLIP, both implemented in IMOD.
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: PEET

+
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