8RHH | pdb_00008rhh

Microtubule-associated kinesin-1 tail complex bound to AMPPNP, two-headed state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Microtubule association induces a Mg-free apo-like ADP pre-release conformation in kinesin-1 that is unaffected by its autoinhibitory tail.

Atherton, J.Chegkazi, M.S.Leusciatti, M.Di Palma, M.Peirano, E.Pozzer, L.S.Meli, M.V.A.Pasqualato, S.Foran, T.Morra, G.Steiner, R.A.

(2025) Nat Commun 16: 6214-6214

  • DOI: https://doi.org/10.1038/s41467-025-61498-3
  • Primary Citation of Related Structures:  
    8RHB, 8RHH, 8RIK, 8RIZ, 9GNQ

  • PubMed Abstract: 

    Kinesin-1 is a processive dimeric ATP-driven motor that transports vital intracellular cargos along microtubules (MTs). If not engaged in active transport, kinesin-1 limits futile ATP hydrolysis by adopting a compact autoinhibited conformation that involves an interaction between its C-terminal tail and the N-terminal motor domains. Here, using a chimeric kinesin-1 that fuses the N-terminal motor region to the tail and a tail variant unable to interact with the motors, we employ cryo-EM to investigate elements of the MT-associated mechanochemical cycle. We describe a missing structure for the proposed two-step allosteric mechanism of ADP release, the ATPase rate limiting step. It shows that MT association remodels the hydrogen bond network at the nucleotide binding site triggering removal of the Mg 2+ ion from the Mg 2+ -ADP complex. This results in a strong MT-binding apo-like state before ADP dissociation, which molecular dynamics simulations indicate is mediated by loop 9 dynamics. We further demonstrate that tail association does not directly affect this mechanism, nor the adoption of the ATP hydrolysis-competent conformation, nor neck linker docking/undocking, even when zippering the two motor domains. We propose a revised mechanism for tail-dependent kinesin-1 autoinhibition and suggest a possible explanation for its characteristic pausing behavior on MTs.


  • Organizational Affiliation
    • Randall Centre for Cell and Molecular Biophysics, King's College London - New Hunt's House, Guy's Campus, London, UK. joseph.atherton@kcl.ac.uk.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chainA [auth B]445Sus 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Kinesin-1 heavy chainB [auth K],
C [auth L],
E [auth T],
F [auth t]
963Homo 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 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP33176
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1B chainD [auth A]451Sus scrofaMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Entity Groups  
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UniProt GroupQ2XVP4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1

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

Download Ideal Coordinates CCD File 
M [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
I [auth K],
L
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GDP
Query on GDP

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

Download Ideal Coordinates CCD File 
J [auth K],
K [auth L],
N [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom206175/Z/17/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/V006568/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/S000828/1

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Data collection
  • Version 1.2: 2025-07-16
    Changes: Data collection, Database references