6DPV

Undecorated GDP microtubule

  • Classification: CELL CYCLE
  • Organism(s): Sus scrofa

  • Deposited: 2018-06-09 Released: 2018-07-04 
  • Deposition Author(s): Zhang, R., Nogales, E.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS); National Science Foundation (NSF, United States); Howard Hughes Medical Institute (HHMI) 

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 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

Separating the effects of nucleotide and EB binding on microtubule structure.

Zhang, R.LaFrance, B.Nogales, E.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E6191-E6200

  • DOI: 10.1073/pnas.1802637115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and are highly regulated by a number of MT-associated pr ...

    Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and are highly regulated by a number of MT-associated proteins (MAPs). How MAPs affect MTs is still not fully understood, partly due to a lack of high-resolution structural data on undecorated MTs, which need to serve as a baseline for further comparisons. Here we report three structures of MTs in different nucleotide states (GMPCPP, GDP, and GTPγS) at near-atomic resolution and in the absence of any binding proteins. These structures allowed us to differentiate the effects of nucleotide state versus MAP binding on MT structure. Kinesin binding has a small effect on the extended, GMPCPP-bound lattice, but hardly affects the compacted GDP-MT lattice, while binding of end-binding (EB) proteins can induce lattice compaction (together with lattice twist) in MTs that were initially in an extended and more stable state. We propose a MT lattice-centric model in which the MT lattice serves as a platform that integrates internal tubulin signals, such as nucleotide state, with outside signals, such as binding of MAPs or mechanical forces, resulting in global lattice rearrangements that in turn affect the affinity of other MT partners and result in the exquisite regulation of MT dynamics.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; zhangrui@wustl.edu enogales@lbl.gov.,Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.,Molecular and Cell Biology Graduate Program, University of California, Berkeley, CA 94720.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
A, C, E, J, K, L
451Sus scrofaMutation(s): 0 
Gene Names: TUBA1B
Find proteins for Q2XVP4 (Sus scrofa)
Go to Gene View: TUBA1B
Go to UniProtKB:  Q2XVP4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
B, D, F, G, H, I
445Sus scrofaMutation(s): 0 
Find proteins for P02554 (Sus scrofa)
Go to UniProtKB:  P02554
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B, D, F, G, H, I
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
A, C, E, J, K, L
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, C, E, J, K, L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.3 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-06-09 
  • Released Date: 2018-07-04 
  • Deposition Author(s): Zhang, R., Nogales, E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM051487
National Science Foundation (NSF, United States)United States1106400
Howard Hughes Medical Institute (HHMI)United States--

Revision History 

  • Version 1.0: 2018-07-04
    Type: Initial release
  • Version 1.1: 2018-07-18
    Type: Data collection, Database references
  • Version 1.2: 2019-11-20
    Type: Author supporting evidence