8SF7

48-nm doublet microtubule from Tetrahymena thermophila strain MEC17


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Effect of alpha-tubulin acetylation on the doublet microtubule structure.

Yang, S.K.Kubo, S.Black, C.S.Peri, K.Dai, D.Legal, T.Valente-Paterno, M.Gaertig, J.Bui, K.H.

(2024) Elife 12

  • DOI: https://doi.org/10.7554/eLife.92219
  • Primary Citation of Related Structures:  
    8SF7

  • PubMed Abstract: 

    Acetylation of α-tubulin at the lysine 40 residue (αK40) by αTAT1/MEC-17 acetyltransferase modulates microtubule properties and occurs in most eukaryotic cells. Previous literatures suggest that acetylated microtubules are more stable and damage resistant. αK40 acetylation is the only known microtubule luminal post-translational modification site. The luminal location suggests that the modification tunes the lateral interaction of protofilaments inside the microtubule. In this study, we examined the effect of tubulin acetylation on the doublet microtubule (DMT) in the cilia of Tetrahymena thermophila using a combination of cryo-electron microscopy, molecular dynamics, and mass spectrometry. We found that αK40 acetylation exerts a small-scale effect on the DMT structure and stability by influencing the lateral rotational angle. In addition, comparative mass spectrometry revealed a link between αK40 acetylation and phosphorylation in cilia.


  • Organizational Affiliation

    Department of Anatomy and Cell Biology, McGill University, Montréal, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NebulinA [auth 6H]518Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RIB27AB [auth 0A],
LB [auth 3A],
OA [auth 2A],
Q [auth 1A]
236Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RIB38C [auth 0B]329Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CFAM166BD [auth 0C],
S [auth 1C]
156Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CFAM166AE [auth 0D],
RA [auth 2D],
T [auth 1D]
225Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
RIB22F [auth 0E],
PB [auth 3E],
SA [auth 2E],
U [auth 1E]
191Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
CFAM166CG [auth 0F]219Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP107H [auth 0G],
W [auth 1G]
183Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP127I [auth 0H],
X [auth 1H]
447Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP161AAB [auth 2N],
DA [auth 1N],
J [auth 0N]
492Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP20195Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Parkin co-regulated protein PACRGAFB [auth 2S],
IA [auth 1S],
L [auth 0S],
WB [auth 3S]
319Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
IJ34GB [auth 2T],
JA [auth 1T],
M [auth 0T],
XB [auth 3T]
298Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 52HB [auth 2U],
KA [auth 1U],
N [auth 0U],
YB [auth 3U]
656Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase delta C4-type zinc-finger proteinIB [auth 2V],
LA [auth 1V],
O [auth 0V],
ZB [auth 3V]
269Tetrahymena thermophilaMutation(s): 0 
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Find proteins for I7M279 (Tetrahymena thermophila (strain SB210))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RIB43A proteinAC [auth 3X],
HC [auth 4X],
KB [auth 2X],
NA [auth 1X],
P [auth 0X]
142Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RIB57MB [auth 3B],
PA [auth 2B],
R [auth 1B]
498Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for I7ME23 (Tetrahymena thermophila (strain SB210))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP182AV [auth 1F]173Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP143Y [auth 1I]263Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP21AZ [auth 1J]422Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 53AA [auth 1K],
XA [auth 2K]
489Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP115BA [auth 1L],
SB [auth 3L],
YA [auth 2L]
940Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinaseCA [auth 1M],
ZA [auth 2M]
372Tetrahymena thermophilaMutation(s): 0 
EC: 2.7.4.6
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Cilia- and flagella-associated protein 45BB [auth 2O],
EA [auth 1O],
TB [auth 3O]
494Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP210CB [auth 2P],
FA [auth 1P]
507Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
RIB72BEB [auth 2R],
HA [auth 1R],
VB [auth 3R]
516Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Protofilament ribbon proteinJB [auth 2W],
MA [auth 1W]
280Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
RIB35BC [auth 4C],
NB [auth 3C],
QA [auth 2C]
300Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP182BTA [auth 2F]96Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Flagellar FliJ proteinUA [auth 2G]99Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
RIB27BDC [auth 4H],
QB [auth 3H],
VA [auth 2H]
229Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
STPG2RB [auth 3I],
WA [auth 2I]
293Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
RIB26OB [auth 3D]237Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP129CC [auth 4F]276Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Flagellar microtugule protofilament ribbon proteinAD [auth 7R],
FC [auth 4R],
UC [auth 5R],
ZC [auth 6R]
613Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Parkin co-regulated protein PACRGBGC [auth 4S],
VC [auth 5S]
249Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
OJ2IC [auth 5A],
JC [auth 5B],
KC [auth 5C],
LC [auth 5D]
175Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP77AMC [auth 5E],
NC [auth 5F],
OC [auth 5G],
PC [auth 5H]
247Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
OJ3QC [auth 5I],
RC [auth 5J],
SC [auth 5K]
168Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
SB1WC [auth 6F]145Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
STPG1AXC [auth 6G]364Tetrahymena thermophilaMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP112BBD [auth 8L],
CD [auth 8N]
385Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
CFAP112ADD [auth 8P],
ED [auth 8R]
363Tetrahymena thermophilaMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha chain449Tetrahymena thermophilaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P41351 (Tetrahymena thermophila)
Explore P41351 
Go to UniProtKB:  P41351
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41351
Sequence Annotations
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  • Reference Sequence
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain443Tetrahymena thermophilaMutation(s): 0 
UniProt
Find proteins for P41352 (Tetrahymena thermophila)
Explore P41352 
Go to UniProtKB:  P41352
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41352
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
ABA [auth OC]
AEA [auth RM]
AHA [auth VI]
AS [auth DA]
AY [auth KG]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
ACA [auth PF]
AFA [auth TB]
AIA [auth WL]
AQ [auth AH]
AT [auth ED]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AAA [auth MN]
ADA [auth QI]
AGA [auth UE]
AR [auth BL]
AU [auth FG]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: CELL 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references
  • Version 1.2: 2024-10-09
    Changes: Data collection, Structure summary