9L7M | pdb_00009l7m

Nucleotide-free kinesin-1 motor domain bound to the microtubule


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping.

Makino, T.Kanada, R.Mori, T.Miyazono, K.I.Komori, Y.Yanagisawa, H.Takada, S.Tanokura, M.Kikkawa, M.Tomishige, M.

(2025) J Cell Biol 224

  • DOI: https://doi.org/10.1083/jcb.202501253
  • Primary Citation of Related Structures:  
    9L6K, 9L78, 9L7E, 9L7M

  • PubMed Abstract: 

    Kinesin-1 walks along microtubules by alternating ATP hydrolysis and movement of its two motor domains ("head"). The detached head preferentially binds to the forward tubulin-binding site after ATP binds to the microtubule-bound head, but the mechanism preventing premature microtubule binding while the partner head awaits ATP remains unknown. Here, we examined the role of the neck linker, the segment connecting two heads, in this mechanism. Structural analyses of the nucleotide-free head revealed a bulge just ahead of the neck linker's base, creating an asymmetric constraint on its mobility. While the neck linker can stretch freely backward, it must navigate around this bulge to extend forward. We hypothesized that increased neck linker tension suppresses premature binding of the tethered head, which was supported by molecular dynamics simulations and single-molecule fluorescence assays. These findings demonstrate a tension-dependent allosteric mechanism that coordinates the movement of two heads, where neck linker tension modulates the allosteric conformational changes rather than directly affecting the nucleotide state.


  • Organizational Affiliation

    Department of Applied Physics, The University of Tokyo, Tokyo, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chain
A, C
451Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2XVP4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chain
B, D
445Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
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UniProt GroupP02554
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-1 heavy chainE [auth K]357Homo sapiensMutation(s): 0 
Gene Names: KIF5BKNSKNS1
UniProt & NIH Common Fund Data Resources
Find proteins for P33176 (Homo sapiens)
Explore P33176 
Go to UniProtKB:  P33176
PHAROS:  P33176
GTEx:  ENSG00000170759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33176
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth A],
I [auth B],
K [auth C],
M [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.48 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-05-21
    Changes: Data collection, Database references