9DGP | pdb_00009dgp

Motor domain of dynein-1 complex on microtubules

PDB DOI: https://doi.org/10.2210/pdb9DGP/pdb
EM Map EMD-46843: EMDB EMDataResource

Classification: MOTOR PROTEIN
Organism(s): Sus scrofa
Mutation(s): No

Deposited: 2024-09-03 Released: 2025-09-10
Deposition Author(s): Rao, Q., Chai, P., Zhang, K.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 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

Molecular basis for the assembly of the dynein transport machinery on microtubules.

Rao, Q., Chai, P., Zhang, K.

(2024) bioRxiv

PubMed: 39803430 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1101/2024.12.30.630772
Primary Citation of Related Structures:
9DGP, 9DGQ, 9DGR, 9DGS, 9DGT, 9DGU, 9DGV

PubMed Abstract:
Cytoplasmic dynein-1, a microtubule-based motor protein, requires dynactin and an adaptor to form the processive dynein-dynactin-adaptor (DDA) complex. The role of microtubules in DDA assembly has been elusive. Here, we reveal detailed structural insights into microtubule-mediated DDA assembly using cryo-electron microscopy. We find that an adaptor-independent dynein-dynactin complex (DD) predominantly forms on microtubules in an intrinsic 2:1 stoichiometry, induced by spontaneous parallelization of dynein upon microtubule binding. Adaptors can squeeze in and exchange within the assembled microtubule-bound DD complex, which is enabled by relative rotations between dynein and dynactin, and further facilitated by dynein light intermediate chains that assist in an adaptor 'search' mechanism. Our findings elucidate the dynamic adaptability of the dynein transport machinery, and reveal a new mode for assembly of the motile complex.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, 06511, USA.

Macromolecule Content

Total Structure Weight: 534.78 kDa
Atom Count: 24,585
Modeled Residue Count: 3,037
Deposited Residue Count: 4,646
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic dynein 1 heavy chain 1	A	4,646	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A287B9W3 (Sus scrofa) Explore A0A287B9W3 Go to UniProtKB: A0A287B9W3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A287B9W3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 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 C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A]	F [auth A], G [auth A], H [auth A], I [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A]