6U0U

Protofilament Ribbon Flagellar Proteins Rib43a-L


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.16 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Tubulin lattice in cilia is in a stressed form regulated by microtubule inner proteins.

Ichikawa, M.Khalifa, A.A.Z.Kubo, S.Dai, D.Basu, K.Maghrebi, M.A.F.Vargas, J.Bui, K.H.

(2019) Proc.Natl.Acad.Sci.USA 116: 19930-19938

  • DOI: 10.1073/pnas.1911119116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around are composed of radially bundled doublet microtubules. In this study, we present a near-atomic resolution map of the <i>Tetrahymena </i> doublet mic ...

    Cilia, the hair-like protrusions that beat at high frequencies to propel a cell or move fluid around are composed of radially bundled doublet microtubules. In this study, we present a near-atomic resolution map of the Tetrahymena doublet microtubule by cryoelectron microscopy. The map demonstrates that the network of microtubule inner proteins weaves into the tubulin lattice and forms an inner sheath. From mass spectrometry data and de novo modeling, we identified Rib43a proteins as the filamentous microtubule inner proteins in the protofilament ribbon region. The Rib43a-tubulin interaction leads to an elongated tubulin dimer distance every 2 dimers. In addition, the tubulin lattice structure with missing microtubule inner proteins (MIPs) by sarkosyl treatment shows significant longitudinal compaction and lateral angle change between protofilaments. These results are evidence that the MIPs directly affect and stabilize the tubulin lattice. It suggests that the doublet microtubule is an intrinsically stressed filament and that this stress could be manipulated in the regulation of ciliary waveforms.


    Organizational Affiliation

    Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada; huy.bui@mcgill.ca.,Facility for Electron Microscopy Research, McGill University, Montréal, QC H3A 0C7, Canada.,Department of Biophysics, Graduate School of Science, Kyoto University, 606-8502 Kyoto, Japan.,Department of Anatomy and Cell Biology, McGill University, Montréal, QC H3A 0C7, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha chain
C, D, E, F, G, H
449Tetrahymena thermophilaMutation(s): 0 
Find proteins for P41351 (Tetrahymena thermophila)
Go to UniProtKB:  P41351
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
B, I, J, K, L, M
443Tetrahymena thermophilaMutation(s): 0 
Gene Names: BTU1, BTU2
Find proteins for P41352 (Tetrahymena thermophila)
Go to UniProtKB:  P41352
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protofilament ribbon protein
A
280Tetrahymena thermophila (strain SB210)Mutation(s): 0 
Find proteins for Q240R7 (Tetrahymena thermophila (strain SB210))
Go to UniProtKB:  Q240R7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B, I, J, K, L, M
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
C, D, E, F, G, H
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
C, D, E, F, G, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.16 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaDG69462
Canadian Institutes of Health Research (CIHR)CanadaPG388933
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2018-04813

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-02
    Type: Data collection, Database references
  • Version 1.2: 2019-10-16
    Type: Data collection, Database references
  • Version 1.3: 2020-01-08
    Type: Author supporting evidence