5GSZ

Crystal Structure of the KIF19A Motor Domain Complexed with Mg-ADP

  • Classification: MOTOR PROTEIN
  • Organism(s): Mus musculus
  • Expression System: Escherichia coli K-12
  • Mutation(s): No 

  • Deposited: 2016-08-18 Released: 2016-09-28 
  • Deposition Author(s): Wang, D., Nitta, R., Hirokawa, N.
  • Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology of Japan, the Ministry of Education, Culture, Sports, Science and Technology of Japan

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Motility and microtubule depolymerization mechanisms of the Kinesin-8 motor, KIF19A

Wang, D.Nitta, R.Morikawa, M.Yajima, H.Inoue, S.Shigematsu, H.Kikkawa, M.Hirokawa, N.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.18101
  • Primary Citation of Related Structures:  
    5GSY, 5GSZ

  • PubMed Abstract: 

    The kinesin-8 motor, KIF19A, accumulates at cilia tips and controls cilium length. Defective KIF19A leads to hydrocephalus and female infertility because of abnormally elongated cilia. Uniquely among kinesins, KIF19A possesses the dual functions of motility along ciliary microtubules and depolymerization of microtubules. To elucidate the molecular mechanisms of these functions we solved the crystal structure of its motor domain and determined its cryo-electron microscopy structure complexed with a microtubule. The features of KIF19A that enable its dual function are clustered on its microtubule-binding side. Unexpectedly, a destabilized switch II coordinates with a destabilized L8 to enable KIF19A to adjust to both straight and curved microtubule protofilaments. The basic clusters of L2 and L12 tether the microtubule. The long L2 with a characteristic acidic-hydrophobic-basic sequence effectively stabilizes the curved conformation of microtubule ends. Hence, KIF19A utilizes multiple strategies to accomplish the dual functions of motility and microtubule depolymerization by ATP hydrolysis.


  • Organizational Affiliation

    Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF19353Mus musculusMutation(s): 0 
Gene Names: Kif19Kif19a
UniProt
Find proteins for Q99PT9 (Mus musculus)
Explore Q99PT9 
Go to UniProtKB:  Q99PT9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99PT9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.604α = 90
b = 122.604β = 90
c = 56.198γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata collection
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education, Culture, Sports, Science and Technology of JapanJapan23000013
the Ministry of Education, Culture, Sports, Science and Technology of JapanJapan15K08168

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-28
    Type: Initial release
  • Version 1.1: 2016-10-12
    Changes: Database references
  • Version 1.2: 2016-10-19
    Changes: Database references
  • Version 1.3: 2020-02-26
    Changes: Data collection, Derived calculations