5MIO | pdb_00005mio

KIF2C-DARPIN FUSION PROTEIN BOUND TO TUBULIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 
    0.257 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.213 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1038/s41467-017-00091-9
  • Primary Citation 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 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
    • Department of Central Laboratory, Shanghai Tenth People's Hospital of Tongji University, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.

Macromolecule Content 

  • Total Structure Weight: 164.24 kDa 
  • Atom Count: 10,421 
  • Modeled Residue Count: 1,329 
  • Deposited Residue Count: 1,469 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain451Bos taurusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P81947 (Bos taurus)
Explore P81947 
Go to UniProtKB:  P81947
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP81947
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta chain445Ovis ariesMutation(s): 0 
UniProt
Find proteins for D0VWY9 (Ovis aries)
Explore D0VWY9 
Go to UniProtKB:  D0VWY9
Entity Groups
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UniProt GroupD0VWY9
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Kinesin-like protein KIF2C,KIF2C FUSED TO A DARPIN,KIF2C FUSED TO A DARPIN573Homo sapiensMutation(s): 2 
Gene Names: KIF2CKNSL6
UniProt & NIH Common Fund Data Resources
Find proteins for Q99661 (Homo sapiens)
Explore Q99661 
Go to UniProtKB:  Q99661
PHAROS:  Q99661
GTEx:  ENSG00000142945 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99661
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
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
I [auth C]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
LOC

Query on LOC



Download:Ideal Coordinates CCD File
G [auth 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
MG

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free:  0.257 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
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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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-12-BSV8-0002-01
Fondation ARCFrancePDF 20130606987

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary