8FDU

Engineered human dynein motor domain in the microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi (local refined on AAA3-AAA5 and LIS1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport.

Ton, W.D.Wang, Y.Chai, P.Beauchamp-Perez, C.Flint, N.T.Lammers, L.G.Xiong, H.Zhang, K.Markus, S.M.

(2023) Nat Struct Mol Biol 30: 1365-1379

  • DOI: https://doi.org/10.1038/s41594-023-01010-x
  • Primary Citation of Related Structures:  
    8FCY, 8FD6, 8FDT, 8FDU

  • PubMed Abstract: 

    The lissencephaly-related protein LIS1 is a critical regulator of cytoplasmic dynein that governs motor function and intracellular localization (for example, to microtubule plus-ends). Although LIS1 binding is required for dynein activity, its unbinding prior to initiation of cargo transport is equally important, since preventing dissociation leads to dynein dysfunction. To understand whether and how dynein-LIS1 binding is modulated, we engineered dynein mutants locked in a microtubule-bound (MT-B) or microtubule-unbound (MT-U) state. Whereas the MT-B mutant exhibits low LIS1 affinity, the MT-U mutant binds LIS1 with high affinity, and as a consequence remains almost irreversibly associated with microtubule plus-ends. We find that a monomeric motor domain is sufficient to exhibit these opposing LIS1 affinities, and that this is evolutionarily conserved between yeast and humans. Three cryo-EM structures of human dynein with and without LIS1 reveal microtubule-binding induced conformational changes responsible for this regulation. Our work reveals key biochemical and structural insight into LIS1-mediated dynein activation.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase3,126Homo sapiensThermus thermophilus HB8Mutation(s): 0 
Gene Names: DYNC1H1DHC1DNCH1DNCLDNECLDYHCKIAA0325serSTTHA0875
EC: 6.1.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SJX7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q5SJX7 
Go to UniProtKB:  Q5SJX7
Find proteins for Q14204 (Homo sapiens)
Explore Q14204 
Go to UniProtKB:  Q14204
PHAROS:  Q14204
GTEx:  ENSG00000197102 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ14204Q5SJX7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet-activating factor acetylhydrolase IB subunit beta,Platelet-activating factor acetylhydrolase IB subunit beta,human LIS1 protein with a SNAP tag
B, C
598Homo sapiensMutation(s): 0 
Gene Names: PAFAH1B1LIS1MDCRMDSPAFAHA
UniProt & NIH Common Fund Data Resources
Find proteins for P43034 (Homo sapiens)
Explore P43034 
Go to UniProtKB:  P43034
PHAROS:  P43034
GTEx:  ENSG00000007168 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43034
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX2.9
RECONSTRUCTIONcryoSPARC3

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM139483
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM142959
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD023603

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-06-28
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-15
    Changes: Database references, Source and taxonomy, Structure summary