[English] 日本語
![](img/lk-miru.gif)
- EMDB-15978: Masked refinement of the IFTB1 subcomplex within anterograde intr... -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Masked refinement of the IFTB1 subcomplex within anterograde intraflagellar trains in Chlamydomonas reinhardtii cilia | |||||||||
![]() | ||||||||||
![]() |
| |||||||||
![]() | Cilia / IFT / Intraflagellar / transport / PROTEIN TRANSPORT | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 9.9 Å | |||||||||
![]() | Lacey SE / Pigino G | |||||||||
Funding support | European Union, ![]()
| |||||||||
![]() | ![]() Title: The molecular structure of IFT-A and IFT-B in anterograde intraflagellar transport trains. Authors: Samuel E Lacey / Helen E Foster / Gaia Pigino / ![]() Abstract: Anterograde intraflagellar transport (IFT) trains are essential for cilia assembly and maintenance. These trains are formed of 22 IFT-A and IFT-B proteins that link structural and signaling cargos to ...Anterograde intraflagellar transport (IFT) trains are essential for cilia assembly and maintenance. These trains are formed of 22 IFT-A and IFT-B proteins that link structural and signaling cargos to microtubule motors for import into cilia. It remains unknown how the IFT-A/-B proteins are arranged into complexes and how these complexes polymerize into functional trains. Here we use in situ cryo-electron tomography of Chlamydomonas reinhardtii cilia and AlphaFold2 protein structure predictions to generate a molecular model of the entire anterograde train. We show how the conformations of both IFT-A and IFT-B are dependent on lateral interactions with neighboring repeats, suggesting that polymerization is required to cooperatively stabilize the complexes. Following three-dimensional classification, we reveal how IFT-B extends two flexible tethers to maintain a connection with IFT-A that can withstand the mechanical stresses present in actively beating cilia. Overall, our findings provide a framework for understanding the fundamental processes that govern cilia assembly. | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 3.8 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 17.1 KB 17.1 KB | Display Display | ![]() |
Images | ![]() | 74.7 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 4.4 KB | ||
Others | ![]() ![]() ![]() | 1.5 MB 49.5 MB 49.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 827.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 827 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
EMDB pages | ![]() ![]() |
---|
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 3.03 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: A masked refinement on the IFTB1 periphery region,...
File | emd_15978_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | A masked refinement on the IFTB1 periphery region, containing the regions corresponding to IFT56 and IFT52/46 heterodimer. Lowpassed to 16 angstrom and with a -1600 A^2 bfactor | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_15978_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_15978_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : Two IFTB repeats from anterograde intraflagellar transport trains...
Entire | Name: Two IFTB repeats from anterograde intraflagellar transport trains within native Chlamydomonas reinhardtii cilia |
---|---|
Components |
|
-Supramolecule #1: Two IFTB repeats from anterograde intraflagellar transport trains...
Supramolecule | Name: Two IFTB repeats from anterograde intraflagellar transport trains within native Chlamydomonas reinhardtii cilia type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 |
---|---|
Source (natural) | Organism: ![]() ![]() |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | subtomogram averaging |
Aggregation state | helical array |
-
Sample preparation
Buffer | pH: 7 / Details: TAP (Tris-Acetate-Phosphate) Media |
---|---|
Vitrification | Cryogen name: ETHANE |
Details | Chlamydomonas reinhardtii cells applied to quantifoil grids and plunge frozen; cilia project out from cell bodies and traverse holes in the carbon film. |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 2.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
-
Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: RELION (ver. 3.1.3), Warp) / Number subtomograms used: 18216 |
---|---|
Extraction | Number tomograms: 600 / Number images used: 18216 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Protocol: FLEXIBLE FIT |
---|