6O2R | pdb_00006o2r

Deacetylated Microtubules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6O2R

This is version 1.3 of the entry. See complete history

Literature

Effects of alpha-tubulin acetylation on microtubule structure and stability.

Eshun-Wilson, L.Zhang, R.Portran, D.Nachury, M.V.Toso, D.B.Lohr, T.Vendruscolo, M.Bonomi, M.Fraser, J.S.Nogales, E.

(2019) Proc Natl Acad Sci U S A 116: 10366-10371

  • DOI: https://doi.org/10.1073/pnas.1900441116
  • Primary Citation Related Structures: 
    6O2Q, 6O2R, 6O2S, 6O2T

  • PubMed Abstract: 

    Acetylation of K40 in α-tubulin is the sole posttranslational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule stabilization is correlative or causative. We have obtained high-resolution cryo-electron microscopy (cryo-EM) reconstructions of pure samples of αTAT1-acetylated and SIRT2-deacetylated microtubules to visualize the structural consequences of this modification and reveal its potential for influencing the larger assembly properties of microtubules. We modeled the conformational ensembles of the unmodified and acetylated states by using the experimental cryo-EM density as a structural restraint in molecular dynamics simulations. We found that acetylation alters the conformational landscape of the flexible loop that contains αK40. Modification of αK40 reduces the disorder of the loop and restricts the states that it samples. We propose that the change in conformational sampling that we describe, at a location very close to the lateral contacts site, is likely to affect microtubule stability and function.


  • Organizational Affiliation
    • Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.

Macromolecule Content 

  • Total Structure Weight: 606.62 kDa 
  • Atom Count: 40,866 
  • Modeled Residue Count: 5,166 
  • Deposited Residue Count: 5,376 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain
A, C, E, J, K
A, C, E, J, K, L
451Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2XVP4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D, F, G, H
B, D, F, G, H, I
445Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02554
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP

Query on GTP



Download:Ideal Coordinates CCD File
AA [auth K]
CA [auth L]
M [auth A]
P [auth C]
S [auth E]
AA [auth K],
CA [auth L],
M [auth A],
P [auth C],
S [auth E],
Y [auth J]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
O [auth B]
R [auth D]
U [auth F]
V [auth G]
W [auth H]
O [auth B],
R [auth D],
U [auth F],
V [auth G],
W [auth H],
X [auth I]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
BA [auth K]
DA [auth L]
N [auth A]
Q [auth C]
T [auth E]
BA [auth K],
DA [auth L],
N [auth A],
Q [auth C],
T [auth E],
Z [auth J]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
RECONSTRUCTIONFREALIGN9.11

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States2016222703

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-22
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations, Refinement description