1IA0 | pdb_00001ia0

KIF1A HEAD-MICROTUBULE COMPLEX STRUCTURE IN ATP-FORM


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.0 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.6 of the entry. See complete history

Literature

Switch-based Mechanism of Kinesin Motors

Kikkawa, M.Sablin, E.P.Okada, Y.Yajima, H.Fletterick, R.J.Hirokawa, N.

(2001) Nature 411: 439-445

  • DOI: https://doi.org/10.1038/35078000
  • Primary Citation Related Structures: 
    1I5S, 1I6I, 1IA0

  • PubMed Abstract: 

    Kinesin motors are specialized enzymes that use hydrolysis of ATP to generate force and movement along their cellular tracks, the microtubules. Although numerous biochemical and biophysical studies have accumulated much data that link microtubule-assisted ATP hydrolysis to kinesin motion, the structural view of kinesin movement remains unclear. This study of the monomeric kinesin motor KIF1A combines X-ray crystallography and cryo-electron microscopy, and allows analysis of force-generating conformational changes at atomic resolution. The motor is revealed in its two functionally critical states-complexed with ADP and with a non-hydrolysable analogue of ATP. The conformational change observed between the ADP-bound and the ATP-like structures of the KIF1A catalytic core is modular, extends to all kinesins and is similar to the conformational change used by myosin motors and G proteins. Docking of the ADP-bound and ATP-like crystallographic models of KIF1A into the corresponding cryo-electron microscopy maps suggests a rationale for the plus-end directional bias associated with the kinesin catalytic core.


  • Organizational Affiliation
    • Department of Cell Biology and Anatomy, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, Japan.

Macromolecule Content 

  • Total Structure Weight: 146.64 kDa 
  • Atom Count: 9,606 
  • Modeled Residue Count: 1,195 
  • Deposited Residue Count: 1,290 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TUBULIN ALPHA CHAIN451Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P02550 (Sus scrofa)
Explore P02550 
Go to UniProtKB:  P02550
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02550
Sequence Annotations
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
TUBULIN BETA CHAIN445Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02554
Sequence Annotations
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
KINESIN-LIKE PROTEIN KIF1AC [auth K]394Mus musculusMutation(s): 1 
Gene Names: KIF1A
EC: 5.6.1.3
UniProt
Find proteins for P33173 (Mus musculus)
Explore P33173 
Go to UniProtKB:  P33173
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33173
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TXL

Query on TXL



Download:Ideal Coordinates CCD File
F [auth B]TAXOTERE
C43 H53 N O14
ZDZOTLJHXYCWBA-VCVYQWHSSA-N
GTP

Query on GTP



Download:Ideal Coordinates CCD File
D [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ACP

Query on ACP



Download:Ideal Coordinates CCD File
H [auth K]PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
C11 H18 N5 O12 P3
UFZTZBNSLXELAL-IOSLPCCCSA-N
GDP

Query on GDP



Download:Ideal Coordinates CCD File
E [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG

Query on MG



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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 15.0 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-03-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2016-04-27
    Changes: Other
  • Version 1.4: 2017-10-04
    Changes: Refinement description
  • Version 1.5: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.6: 2024-12-25
    Changes: Advisory, Data collection, Derived calculations, Refinement description, Structure summary