3JAK

Cryo-EM structure of GTPgammaS-microtubule co-polymerized with EB3 (merged dataset with and without kinesin bound)


Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1016/j.cell.2015.07.012
  • Primary Citation of Related Structures:  
    3JAK, 3JAL, 3JAR, 3JAS, 3JAT, 3JAW

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain451Sus 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
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain445Sus 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
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Microtubule-associated protein RP/EB family member 3C [auth N],
L [auth M]
203Homo sapiensMutation(s): 0 
Gene Names: MAPRE3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPY8 (Homo sapiens)
Explore Q9UPY8 
Go to UniProtKB:  Q9UPY8
PHAROS:  Q9UPY8
GTEx:  ENSG00000084764 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UPY8
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSP
Query on GSP

Download Ideal Coordinates CCD File 
CA [auth B]
FA [auth H]
Q [auth F]
T [auth G]
W [auth D]
CA [auth B],
FA [auth H],
Q [auth F],
T [auth G],
W [auth D],
Z [auth I]
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
GTP
Query on GTP

Download Ideal Coordinates CCD File 
AA [auth A]
DA [auth K]
O [auth E]
R [auth J]
U [auth C]
AA [auth A],
DA [auth K],
O [auth E],
R [auth J],
U [auth C],
X [auth L]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth A]
EA [auth K]
P [auth E]
S [auth J]
V [auth C]
BA [auth A],
EA [auth K],
P [auth E],
S [auth J],
V [auth C],
Y [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONEMAN1
RECONSTRUCTIONFREALIGN

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-12
    Type: Initial release
  • Version 1.1: 2015-09-02
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-18
    Changes: Database references, Other
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description