9E0X | pdb_00009e0x

Cryo-EM structure of Phi dynein

PDB DOI: https://doi.org/10.2210/pdb9E0X/pdb
EM Map EMD-47373: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-10-20 Released: 2025-07-09
Deposition Author(s): Nguyen, K.H.V., Kendrick, A.A., Leschziner, A.E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM captures early intermediate steps in dynein activation by LIS1.

Nguyen, K.H.V., Karasmanis, E.P., Kendrick, A.A., Reck-Peterson, S.L., Leschziner, A.E.

(2025) Nat Commun 16: 7054-7054

PubMed: 40750582 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-62185-z
Primary Citation Related Structures:
9DZY, 9E0K, 9E0T, 9E0U, 9E0W, 9E0X, 9E0Y, 9E22, 9E23, 9E28

PubMed Abstract:
Cytoplasmic dynein-1 (dynein) is an essential molecular motor in eukaryotic cells. Dynein primarily exists in an autoinhibited Phi state and requires conformational changes to assemble with its cofactors and form active transport complexes. LIS1, a key dynein regulator, enhances dynein activation and assembly. Using cryo-EM and a human dynein-LIS1 sample incubated with ATP, we map the conformational landscape of dynein activation by LIS1 and identify an early intermediate state that we propose precedes the previously identified dynein-LIS1 Chi state. Mutations that disrupt this species, which we termed "Pre-Chi", lead to motility defects in vitro, emphasizing its functional importance. Together, our findings provide insights into how LIS1 relieves dynein autoinhibition during the activation pathway.

Organizational Affiliation

Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.

Macromolecule Content

Total Structure Weight: 1,111.93 kDa
Atom Count: 46,234
Modeled Residue Count: 5,840
Deposited Residue Count: 9,686
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic dynein 1 heavy chain 1	A, B	4,843	Homo sapiens	Mutation(s): 0 Gene Names: DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325
UniProt & NIH Common Fund Data Resources
Find proteins for Q14204 (Homo sapiens) Explore Q14204 Go to UniProtKB: Q14204
PHAROS: Q14204 GTEx: ENSG00000197102
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q14204
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain J [auth B]	D [auth A], J [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain C [auth A]	C [auth A] E [auth A] F [auth A] I [auth B] K [auth B] C [auth A], E [auth A], F [auth A], I [auth B], K [auth B], L [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	G [auth A], H [auth A], M [auth B], N [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-07-09

Deposition Author(s):

Nguyen, K.H.V.

Kendrick, A.A.

Leschziner, A.E.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM139795
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM145296