[English] 日本語
Yorodumi
- EMDB-20066: Three-dimensional architecture of epithelial primary cilia -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: EMD-20066
TitleThree-dimensional architecture of epithelial primary cilia
Map data
Sampleprimary cilium #D
SourceMus musculus (house mouse)
Methodelectron tomography / negative staining
AuthorsSun S / Fisher RL / Bowser SS / Pentecost BT / Sui H
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Three-dimensional architecture of epithelial primary cilia.
Authors: Shufeng Sun / Rebecca L Fisher / Samuel S Bowser / Brian T Pentecost / Haixin Sui /
Abstract: We report a complete 3D structural model of typical epithelial primary cilia based on structural maps of full-length primary cilia obtained by serial section electron tomography. Our data demonstrate ...We report a complete 3D structural model of typical epithelial primary cilia based on structural maps of full-length primary cilia obtained by serial section electron tomography. Our data demonstrate the architecture of primary cilia differs extensively from the commonly acknowledged 9+0 paradigm. The axoneme structure is relatively stable but gradually evolves from base to tip with a decreasing number of microtubule complexes (MtCs) and a reducing diameter. The axonemal MtCs are cross-linked by previously unrecognized fibrous protein networks. Such an architecture explains why primary cilia can elastically withstand liquid flow for mechanosensing. The nine axonemal MtCs in a cilium are found to differ significantly in length indicating intraflagellar transport processes in primary cilia may be more complicated than that reported for motile cilia. The 3D maps of microtubule doublet-singlet transitions generally display longitudinal gaps at the inner junction between the A- and B-tubules, which indicates the inner junction protein is a major player in doublet-singlet transitions. In addition, vesicles releasing from kidney primary cilia were observed in the structural maps, supporting that ciliary vesicles budding may serve as ectosomes for cell-cell communication.
DateDeposition: Apr 6, 2019 / Header (metadata) release: May 1, 2019 / Map release: May 1, 2019 / Update: May 22, 2019

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_20066.map.gz / Format: CCP4 / Size: 604.7 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 12.82 Å
Density
Minimum - Maximum0.0 - 127.0
Average (Standard dev.)82.980400000000003 (±4.3376336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin12811136-93
Dimensions1024720860
Spacing7201024860
CellA: 9230.399 Å / B: 13127.68 Å / C: 11025.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z12.81999861111112.8212.82
M x/y/z7201024860
origin x/y/z0.0000.0000.000
length x/y/z9230.39913127.68011025.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S123
start NC/NR/NS11361281-93
NC/NR/NS7201024860
D min/max/mean0.000127.00082.980

-
Supplemental data

-
Sample components

-
Entire primary cilium #D

EntireName: primary cilium #D
Details: IMCD3 primary cilium #D is related to Fig.S3d, Fig.S4d, and movie 9.
Number of components: 1

-
Component #1: cellular-component, primary cilium #D

Cellular-componentName: primary cilium #D
Details: IMCD3 primary cilium #D is related to Fig.S3d, Fig.S4d, and movie 9.
Recombinant expression: No
SourceSpecies: Mus musculus (house mouse)
Source (natural)Cell: IMCD3 / Organ or tissue: kidney

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Cell / Method: negative staining
Sample solutionBuffer solution: PBS / pH: 7.4
Support filmunspecified
Staining2% uranyl acetate and Reynolds lead citrate solution
VitrificationCryogen name: NONE

-
Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 6 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

-
Image processing

ProcessingMethod: electron tomography / Number of sections: 3276
3D reconstructionSoftware: TOMO3D
Details: This SSET work used a series of dual-axis tilt data sets.

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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