3JAR

Cryo-EM structure of GDP-microtubule co-polymerized with EB3

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins.

Zhang, R., Alushin, G.M., Brown, A., Nogales, E.

(2015) Cell 162: 849-859

  • DOI: 10.1016/j.cell.2015.07.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo-electron microscopy (cryo-EM) structures of MTs, at ...

    Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo-electron microscopy (cryo-EM) structures of MTs, at 3.5 Å or better resolution, bound to GMPCPP, GTPγS, or GDP, either decorated with kinesin motor domain after polymerization or copolymerized with EB3. Subtle changes around the E-site nucleotide during hydrolysis trigger conformational changes in α-tubulin around an "anchor point," leading to global lattice rearrangements and strain generation. Unlike the extended lattice of the GMPCPP-MT, the EB3-bound GTPγS-MT has a compacted lattice that differs in lattice twist from that of the also compacted GDP-MT. These results and the observation that EB3 promotes rapid hydrolysis of GMPCPP suggest that EB proteins modulate structural transitions at growing MT ends by recognizing and promoting an intermediate state generated during GTP hydrolysis. Our findings explain both EBs end-tracking behavior and their effect on microtubule dynamics.

    Organizational Affiliation: 

    Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
E, J, C, L, A, K
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
F, G, D, I, B, H
445Sus scrofaMutation(s): 0 
Find proteins for P02554 (Sus scrofa)
Go to UniProtKB:  P02554
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Microtubule-associated protein RP/EB family member 3
N, M
203Homo sapiensMutation(s): 0 
Gene Names: MAPRE3
Find proteins for Q9UPY8 (Homo sapiens)
Go to Gene View: MAPRE3
Go to UniProtKB:  Q9UPY8
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: 3.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2015-06-19 
  • Released Date: 2015-08-12 
  • Deposition Author(s): Zhang, R., Nogales, E.

Revision History 

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Author supporting evidence, Data collection