6O2T

Acetylated Microtubules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: 10.1073/pnas.1900441116
  • Primary Citation of Related Structures:  
    6O2R, 6O2Q, 6O2T, 6O2S

  • 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 ...

    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

    Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.



Macromolecules
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
AD [auth 1A] , AG [auth 3A] , BF [auth 2I] , BI [auth 4I] , CD [auth 1B] , CG [auth 3B] , DF [auth 2J] , DI [auth 4J] , 
AD [auth 1A],  AG [auth 3A],  BF [auth 2I],  BI [auth 4I],  CD [auth 1B],  CG [auth 3B],  DF [auth 2J],  DI [auth 4J],  ED [auth 1C],  EG [auth 3C],  FF [auth 2K],  FI [auth 4K],  GD [auth 1D],  GG [auth 3D],  HF [auth 2L],  HI [auth 4L],  ID [auth 1E],  IG [auth 3E],  JF [auth 2M],  JI [auth 4M],  KD [auth 1F],  KG [auth 3F],  LF [auth 2N],  LI [auth 4N],  MD [auth 1G],  MG [auth 3G],  NE [auth 2A],  NH [auth 4A],  OD [auth 1I],  OG [auth 3I],  PE [auth 2B],  PH [auth 4B],  QD [auth 1J],  QG [auth 3J],  RE [auth 2C],  RH [auth 4C],  SD [auth 1K],  SG [auth 3K],  TE [auth 2D],  TH [auth 4D],  UD [auth 1L],  UG [auth 3L],  VE [auth 2E],  VH [auth 4E],  WD [auth 1M],  WG [auth 3M],  XE [auth 2F],  XH [auth 4F],  YD [auth 1N],  YG [auth 3N],  ZE [auth 2G],  ZH [auth 4G]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
AE [auth 1H] , AH [auth 3H] , BE [auth 1O] , BH [auth 3O] , CE [auth 1P] , CH [auth 3P] , DE [auth 1Q] , DH [auth 3Q] , 
AE [auth 1H],  AH [auth 3H],  BE [auth 1O],  BH [auth 3O],  CE [auth 1P],  CH [auth 3P],  DE [auth 1Q],  DH [auth 3Q],  EE [auth 1R],  EH [auth 3R],  FE [auth 1S],  FH [auth 3S],  GE [auth 1T],  GH [auth 3T],  HE [auth 1U],  HH [auth 3U],  IE [auth 1V],  IH [auth 3V],  JE [auth 1W],  JH [auth 3W],  KE [auth 1X],  KH [auth 3X],  LE [auth 1Y],  LH [auth 3Y],  ME [auth 1Z],  MH [auth 3Z],  NF [auth 2H],  NI [auth 4H],  OF [auth 2O],  OI [auth 4O],  PF [auth 2P],  PI [auth 4P],  QF [auth 2Q],  QI [auth 4Q],  RF [auth 2R],  RI [auth 4R],  SF [auth 2S],  SI [auth 4S],  TF [auth 2T],  TI [auth 4T],  UF [auth 2U],  UI [auth 4U],  VF [auth 2V],  VI [auth 4V],  WF [auth 2W],  WI [auth 4W],  XF [auth 2X],  XI [auth 4X],  YF [auth 2Y],  YI [auth 4Y],  ZF [auth 2Z],  ZI [auth 4Z]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
AF [auth 2G] , AI [auth 4G] , BD [auth 1A] , BG [auth 3A] , CF [auth 2I] , CI [auth 4I] , DD [auth 1B] , DG [auth 3B] , 
AF [auth 2G],  AI [auth 4G],  BD [auth 1A],  BG [auth 3A],  CF [auth 2I],  CI [auth 4I],  DD [auth 1B],  DG [auth 3B],  EF [auth 2J],  EI [auth 4J],  FD [auth 1C],  FG [auth 3C],  GF [auth 2K],  GI [auth 4K],  HD [auth 1D],  HG [auth 3D],  IF [auth 2L],  II [auth 4L],  JD [auth 1E],  JG [auth 3E],  KF [auth 2M],  KI [auth 4M],  LD [auth 1F],  LG [auth 3F],  MF [auth 2N],  MI [auth 4N],  ND [auth 1G],  NG [auth 3G],  OE [auth 2A],  OH [auth 4A],  PD [auth 1I],  PG [auth 3I],  QE [auth 2B],  QH [auth 4B],  RD [auth 1J],  RG [auth 3J],  SE [auth 2C],  SH [auth 4C],  TD [auth 1K],  TG [auth 3K],  UE [auth 2D],  UH [auth 4D],  VD [auth 1L],  VG [auth 3L],  WE [auth 2E],  WH [auth 4E],  XD [auth 1M],  XG [auth 3M],  YE [auth 2F],  YH [auth 4F],  ZD [auth 1N],  ZG [auth 3N]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

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