4ETP | pdb_00004etp

C-terminal motor and motor homology domain of Kar3Vik1 fused to a synthetic heterodimeric coiled coil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Kar3Vik1, a member of the kinesin-14 superfamily, shows a novel kinesin microtubule binding pattern.

Rank, K.C.Chen, C.J.Cope, J.Porche, K.Hoenger, A.Gilbert, S.P.Rayment, I.

(2012) J Cell Biol 197: 957-970

  • DOI: https://doi.org/10.1083/jcb.201201132
  • Primary Citation Related Structures: 
    4ETP

  • PubMed Abstract: 

    Kinesin-14 motors generate microtubule minus-end-directed force used in mitosis and meiosis. These motors are dimeric and operate with a nonprocessive powerstroke mechanism, but the role of the second head in motility has been unclear. In Saccharomyces cerevisiae, the Kinesin-14 Kar3 forms a heterodimer with either Vik1 or Cik1. Vik1 contains a motor homology domain that retains microtubule binding properties but lacks a nucleotide binding site. In this case, both heads are implicated in motility. Here, we show through structural determination of a C-terminal heterodimeric Kar3Vik1, electron microscopy, equilibrium binding, and motility that at the start of the cycle, Kar3Vik1 binds to or occludes two αβ-tubulin subunits on adjacent protofilaments. The cycle begins as Vik1 collides with the microtubule followed by Kar3 microtubule association and ADP release, thereby destabilizing the Vik1-microtubule interaction and positioning the motor for the start of the powerstroke. The results indicate that head-head communication is mediated through the adjoining coiled coil.


  • Organizational Affiliation
    • Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA.

Macromolecule Content 

  • Total Structure Weight: 85.06 kDa 
  • Atom Count: 5,681 
  • Modeled Residue Count: 666 
  • Deposited Residue Count: 736 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinesin-like protein KAR3403Saccharomyces cerevisiae S288CMutation(s): 5 
Gene Names: KAR3kar3pP9659.16YPR141C
EC: 5.6.1.4
UniProt
Find proteins for P17119 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17119 
Go to UniProtKB:  P17119
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17119
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Spindle pole body-associated protein VIK1333Saccharomyces cerevisiae S288CMutation(s): 7 
Gene Names: VIK1Vik1pYPL253C
UniProt
Find proteins for Q12045 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q12045 
Go to UniProtKB:  Q12045
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12045
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
EBC

Query on EBC



Download:Ideal Coordinates CCD File
J [auth B]N,N'-ethane-1,2-diylbis(2-iodoacetamide)
C6 H10 I2 N2 O2
RLFPCLMBTQOMLI-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.245 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.06α = 90
b = 94.939β = 90
c = 114.59γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 1.1: 2013-08-07
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-11-20
    Changes: Structure summary