3EDL

Kinesin13-Microtubule Ring complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 28.0 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of the kinesin13-microtubule ring complex.

Tan, D.Rice, W.J.Sosa, H.

(2008) Structure 16: 1732-1739

  • DOI: 10.1016/j.str.2008.08.017
  • Primary Citation of Related Structures:  
    3EDL

  • PubMed Abstract: 
  • To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron microscopy (cryo-EM) and image analysis. An atomic model of the complex was produced by docking the crystal structures of tubulin and a kinesin13 motor domain (MD) into the 3D map ...

    To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron microscopy (cryo-EM) and image analysis. An atomic model of the complex was produced by docking the crystal structures of tubulin and a kinesin13 motor domain (MD) into the 3D map. The model reveals a snapshot of the depolymerization mechanism by providing a 3D view of the complex formed between the kinesin13 MD and a curved tubulin protofilament (pf). It suggests that contacts mediated by kinesin13 class-specific residues in the putative microtubule-binding site stabilize intra-dimer tubulin curvature. In addition, a tubulin-binding site on the kinesin13 MD was identified. Mutations at this class-conserved site selectively disrupt the formation of microtubule-associated ring complexes.


    Organizational Affiliation

    Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx NY, 10461, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1A chainA451Bos taurusMutation(s): 0 
Find proteins for P02550 (Sus scrofa)
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Go to UniProtKB:  P02550
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beta tubulinB, E [auth G]445Bos taurusMutation(s): 0 
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF2CC [auth D]331Drosophila melanogasterMutation(s): 0 
Gene Names: DmKlp10A
Find proteins for Q922S8 (Mus musculus)
Explore Q922S8 
Go to UniProtKB:  Q922S8
NIH Common Fund Data Resources
IMPC:  MGI:1921054
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1A chainD [auth F]451Bos taurusMutation(s): 0 
Gene Names: TUBA1D
Find proteins for Q2HJ86 (Bos taurus)
Explore Q2HJ86 
Go to UniProtKB:  Q2HJ86
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1

Download Ideal Coordinates CCD File 
J [auth B]TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
 Ligand Interaction
GTP
Query on GTP

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H [auth B], N [auth F]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ANP
Query on ANP

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L [auth D]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
GDP
Query on GDP

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I [auth B], O [auth F]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
CN2
Query on CN2

Download Ideal Coordinates CCD File 
P [auth G]2-MERCAPTO-N-[1,2,3,10-TETRAMETHOXY-9-OXO-5,6,7,9-TETRAHYDRO-BENZO[A]HEPTALEN-7-YL]ACETAMIDE
C22 H25 N O6 S
TYDIWMTWTXFWSY-HNNXBMFYSA-N
 Ligand Interaction
ZN
Query on ZN

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F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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G [auth A], K [auth D], M [auth F]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 28.0 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-01-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-07-18
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-06-24
    Changes: Database references, Source and taxonomy, Structure summary