5MIO

KIF2C-DARPIN FUSION PROTEIN BOUND TO TUBULIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


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


Literature

Insight into microtubule disassembly by kinesin-13s from the structure of Kif2C bound to tubulin.

Wang, W., Cantos-Fernandes, S., Lv, Y., Kuerban, H., Ahmad, S., Wang, C., Gigant, B.

(2017) Nat Commun 8: 70-70

  • DOI: 10.1038/s41467-017-00091-9
  • Primary Citation of Related Structures:  
    5MIO

  • PubMed Abstract: 

    • Kinesin-13s are critical microtubule regulators which induce microtubule disassembly in an ATP dependent manner. To clarify their mechanism, we report here the crystal structure of a functional construct of the kinesin-13 Kif2C/MCAK in an ATP-like state ...

    Kinesin-13s are critical microtubule regulators which induce microtubule disassembly in an ATP dependent manner. To clarify their mechanism, we report here the crystal structure of a functional construct of the kinesin-13 Kif2C/MCAK in an ATP-like state and bound to the αβ-tubulin heterodimer, a complex mimicking the species that dissociates from microtubule ends during catalytic disassembly. Our results picture how Kif2C stabilizes a curved tubulin conformation. The Kif2C α4-L12-α5 region undergoes a remarkable 25° rotation upon tubulin binding to target the αβ-tubulin hinge. This movement leads the β5a-β5b motif to interact with the distal end of β-tubulin, whereas the neck and the KVD motif, two specific elements of kinesin-13s, target the α-tubulin distal end. Taken together with the study of Kif2C mutants, our data suggest that stabilization of a curved tubulin is an important contribution to the Kif2C mechanism.Kinesin-13s are microtubule depolymerizing enzymes. Here the authors present the crystal structure of a DARPin fused construct comprising the short neck region and motor domain of kinesin-13 in complex with an αβ-tubulin heterodimer, which shows that kinesin-13 functions by stabilizing a curved tubulin conformation.

    Organizational Affiliation: 

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France. benoit.gigant@i2bc.paris-saclay.fr.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chain A451Bos taurusMutation(s): 0 
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chain B445Ovis ariesMutation(s): 0 
Find proteins for D0VWY9 (Ovis aries)
Explore D0VWY9 
Go to UniProtKB:  D0VWY9
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF2C,KIF2C FUSED TO A DARPIN,KIF2C FUSED TO A DARPIN C573Homo sapiensMutation(s): 2 
Gene Names: KIF2C, KNSL6
Find proteins for Q99661 (Homo sapiens)
Explore Q99661 
Go to UniProtKB:  Q99661
NIH Common Fund Data Resources
PHAROS:  Q99661
GTEx:  ENSG00000142945
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
ANP
Query on ANP
Download Ideal Coordinates CCD File 
C
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
LOC
Query on LOC
Download Ideal Coordinates CCD File 
B
N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide
C22 H25 N O6
IAKHMKGGTNLKSZ-INIZCTEOSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
A, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.81α = 90
b = 229.76β = 90
c = 293.95γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-11-28 
  • Released Date: 2017-07-19 
    • Deposition Author(s): Wang, W., Gigant, B.
Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-12-BSV8-0002-01
Fondation ARCFrancePDF 20130606987

Revision History 

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.2: 2019-06-12
    Changes: Data collection, Structure summary