5DJN | pdb_00005djn

Crystal structure of the Kinesin-3 KIF13A NC-CC1 mutant - Deletion of P390


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free: 
    0.233 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural Correlation of the Neck Coil with the Coiled-coil (CC1)-Forkhead-associated (FHA) Tandem for Active Kinesin-3 KIF13A

Ren, J.Huo, L.Wang, W.Zhang, Y.Li, W.Lou, J.Xu, T.Feng, W.

(2016) J Biological Chem 291: 3581-3594

  • DOI: https://doi.org/10.1074/jbc.M115.689091
  • Primary Citation Related Structures: 
    5DJN, 5DJO

  • PubMed Abstract: 

    Processive kinesin motors often contain a coiled-coil neck that controls the directionality and processivity. However, the neck coil (NC) of kinesin-3 is too short to form a stable coiled-coil dimer. Here, we found that the coiled-coil (CC1)-forkhead-associated (FHA) tandem (that is connected to NC by Pro-390) of kinesin-3 KIF13A assembles as an extended dimer. With the removal of Pro-390, the NC-CC1 tandem of KIF13A unexpectedly forms a continuous coiled-coil dimer that can be well aligned into the CC1-FHA dimer. The reverse introduction of Pro-390 breaks the NC-CC1 coiled-coil dimer but provides the intrinsic flexibility to couple NC with the CC1-FHA tandem. Mutations of either NC, CC1, or the FHA domain all significantly impaired the motor activity. Thus, the three elements within the NC-CC1-FHA tandem of KIF13A are structurally interrelated to form a stable dimer for activating the motor. This work also provides the first direct structural evidence to support the formation of a coiled-coil neck by the short characteristic neck domain of kinesin-3.


  • Organizational Affiliation
    • From the National Laboratory of Biomacromolecules and.

Macromolecule Content 

  • Total Structure Weight: 21.41 kDa 
  • Atom Count: 1,299 
  • Modeled Residue Count: 158 
  • Deposited Residue Count: 188 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinesin-like proteinA,
B [auth C]
94Mus musculusMutation(s): 0 
Gene Names: Kif13a
UniProt & NIH Common Fund Data Resources
Find proteins for F8VQ75 (Mus musculus)
Explore F8VQ75 
Go to UniProtKB:  F8VQ75
IMPC:  MGI:1098264
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF8VQ75
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.82 Å
  • R-Value Free:  0.233 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.62α = 90
b = 158.62β = 90
c = 82.52γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
xia2data scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-02-24
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations