Skip to main content

 7TR3 | pdb_00007tr3

CaKip3[2-482] - AMP-PNP in complex with a dolastatin-10-stabilized tubulin ring


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7TR3

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

Literature

Kinesin-8-specific loop-2 controls the dual activities of the motor domain according to tubulin protofilament shape.

Hunter, B., Benoit, M.P.M.H., Asenjo, A.B., Doubleday, C., Trofimova, D., Frazer, C., Shoukat, I., Sosa, H., Allingham, J.S.

(2022) Nat Commun 13: 4198-4198

  • DOI: https://doi.org/10.1038/s41467-022-31794-3
  • Primary Citation Related Structures: 
    7LFF, 7TQX, 7TQY, 7TQZ, 7TR0, 7TR1, 7TR2, 7TR3

  • PubMed Abstract: 

    Kinesin-8s are dual-activity motor proteins that can move processively on microtubules and depolymerize microtubule plus-ends, but their mechanism of combining these distinct activities remains unclear. We addressed this by obtaining cryo-EM structures (2.6-3.9 Å) of Candida albicans Kip3 in different catalytic states on the microtubule lattice and on a curved microtubule end mimic. We also determined a crystal structure of microtubule-unbound CaKip3-ADP (2.0 Å) and analyzed the biochemical activity of CaKip3 and kinesin-1 mutants. These data reveal that the microtubule depolymerization activity of kinesin-8 originates from conformational changes of its motor core that are amplified by dynamic contacts between its extended loop-2 and tubulin. On curved microtubule ends, loop-1 inserts into preceding motor domains, forming head-to-tail arrays of kinesin-8s that complement loop-2 contacts with curved tubulin and assist depolymerization. On straight tubulin protofilaments in the microtubule lattice, loop-2-tubulin contacts inhibit conformational changes in the motor core, but in the ADP-Pi state these contacts are relaxed, allowing neck-linker docking for motility. We propose that these tubulin shape-induced alternations between pro-microtubule-depolymerization and pro-motility kinesin states, regulated by loop-2, are the key to the dual activity of kinesin-8 motors.


  • Organizational Affiliation: 
    • Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.

Macromolecule Content 

  • Total Structure Weight: 157.36 kDa 
  • Atom Count: 10,222 
  • Modeled Residue Count: 1,288 
  • Deposited Residue Count: 1,387 
  • Unique protein chains: 3

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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta-2B 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
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinesin-like proteinC [auth K]491Candida albicansMutation(s): 0 
Gene Names: KIP3, orf19.7353, CAALFM_C305720CA
UniProt
Find proteins for A0A1D8PKA4 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore A0A1D8PKA4 
Go to UniProtKB:  A0A1D8PKA4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D8PKA4
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SR6
(Subject of Investigation/LOI)

Query on SR6



Download:Ideal Coordinates CCD File
G [auth B]dolastatin-10
C42 H68 N6 O6 S
OFDNQWIFNXBECV-VFSYNPLYSA-N
GTP

Query on GTP



Download:Ideal Coordinates CCD File
D [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ANP

Query on ANP



Download:Ideal Coordinates CCD File
H [auth K]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
F [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM113164
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN/356025-2013
Canadian Institutes of Health Research (CIHR)CanadaMOP-97832

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-08-10
    Changes: Database references
  • Version 1.2: 2024-02-21
    Changes: Data collection