3JAT | pdb_00003jat

Cryo-EM structure of GMPCPP-microtubule (14 protofilaments) decorated with kinesin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 3JAT

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 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.

Macromolecule Content 

  • Total Structure Weight: 607.23 kDa 
  • Atom Count: 40,500 
  • Modeled Residue Count: 5,124 
  • 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 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
Find similar proteins by:|  3D Structure
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

Small Molecules

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

Query on GTP



Download:Ideal Coordinates CCD File
CA [auth A]
GA [auth K]
M [auth E]
Q [auth J]
U [auth C]
CA [auth A],
GA [auth K],
M [auth E],
Q [auth J],
U [auth C],
Y [auth L]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
G2P

Query on G2P



Download:Ideal Coordinates CCD File
AA [auth I]
EA [auth B]
IA [auth H]
O [auth F]
S [auth G]
AA [auth I],
EA [auth B],
IA [auth H],
O [auth F],
S [auth G],
W [auth D]
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
GXTIEXDFEKYVGY-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
BA [auth I]
DA [auth A]
FA [auth B]
HA [auth K]
JA [auth H]
BA [auth I],
DA [auth A],
FA [auth B],
HA [auth K],
JA [auth H],
N [auth E],
P [auth F],
R [auth J],
T [auth G],
V [auth C],
X [auth D],
Z [auth L]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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: 2015-09-09
    Changes: Database references
  • Version 1.2: 2018-07-18
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2019-12-18
    Changes: Other
  • Version 1.4: 2024-02-21
    Changes: Data collection, Database references, Derived calculations, Refinement description