2HXH

KIF1A head-microtubule complex structure in adp-form

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations

Kikkawa, M., Hirokawa, N.

(2006) EMBO J 25: 4187-4194

  • DOI: 10.1038/sj.emboj.7601299
  • Primary Citation of Related Structures:  
    2HXF, 2HXH

  • PubMed Abstract: 

    • Kinesin is an ATP-driven microtubule (MT)-based motor fundamental to organelle transport. Although a number of kinesin crystal structures have been solved, the structural evidence for coupling between the bound nucleotide and the conformation of kinesin is elusive ...

    Kinesin is an ATP-driven microtubule (MT)-based motor fundamental to organelle transport. Although a number of kinesin crystal structures have been solved, the structural evidence for coupling between the bound nucleotide and the conformation of kinesin is elusive. In addition, the structural basis of the MT-induced ATPase activity of kinesin is not clear because of the absence of the MT in the structure. Here, we report cryo-electron microscopy structures of the monomeric kinesin KIF1A-MT complex in two nucleotide states at about 10 A resolution, sufficient to reveal the secondary structure. These high-resolution maps visualized clear structural changes that suggest a mechanical pathway from the nucleotide to the neck linker via the motor core rotation. In addition, new nucleotide binding pocket conformations are observed that are different from X-ray crystallographic structures; it is closed in the 5'-adenylyl-imidodiphosphate state, but open in the ADP state. These results suggest a structural model of biased diffusion movement of monomeric kinesin motor.

    Organizational Affiliation: 

    Department of Cell Biology, Southwestern Medical Center, University of Texas, Dallas, TX, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha chainA451Sus scrofaMutation(s): 0 
Gene Names: TUBA1A
UniProt
Find proteins for P02550 (Sus scrofa)
Explore P02550 
Go to UniProtKB:  P02550
Entity Groups  
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UniProt GroupP02550
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainB445Sus 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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein KIF1AC394Mus musculusMutation(s): 1 
Gene Names: Kif1a, Atsv, Kif1
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1
Download Ideal Coordinates CCD File 
G [auth B]TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N		 Ligand Interaction
GTP
Query on GTP
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E [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
F [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
ADP
Query on ADP
Download Ideal Coordinates CCD File 
I [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
H [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TA1 BindingDB:  2HXH EC50: 520 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 11.0 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-12-18
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.4: 2021-11-10
    Changes: Database references, Derived calculations