9YNC | pdb_00009ync

Motor domains of phi-like human dynein-1 bound to dynactin-p150glued and LIS1

PDB DOI: https://doi.org/10.2210/pdb9YNC/pdb
EM Map EMD-73173: EMDB EMDataResource

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

Deposited: 2025-10-10 Released: 2026-01-28
Deposition Author(s): Yang, J., 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: 3.93 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

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

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

To be published.

Macromolecule Content

Total Structure Weight: 1,683.81 kDa
Atom Count: 56,882
Modeled Residue Count: 7,224
Deposited Residue Count: 14,770
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic dynein 1 heavy chain 1	A, B	4,646	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q14204
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Platelet-activating factor acetylhydrolase IB subunit beta	C, D, E, F	410	Homo sapiens	Mutation(s): 0 Gene Names: PAFAH1B1, LIS1, MDCR, MDS, PAFAHA
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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43034
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic dynein 1 intermediate chain 2	G, H	638	Homo sapiens	Mutation(s): 0 Gene Names: DYNC1I2, DNCI2, DNCIC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13409 (Homo sapiens) Explore Q13409 Go to UniProtKB: Q13409
PHAROS: Q13409 GTEx: ENSG00000077380
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13409
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Dynactin subunit 1	I, J	1,281	Sus scrofa	Mutation(s): 0 Gene Names: DCTN1
UniProt
Find proteins for A0A287B8J2 (Sus scrofa) Explore A0A287B8J2 Go to UniProtKB: A0A287B8J2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A287B8J2
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 L [auth A] SDF format, chain R [auth B] MOL2 format, chain L [auth A] MOL2 format, chain R [auth B] mmCIF format, chain L [auth A] mmCIF format, chain R [auth B]	L [auth A], R [auth B]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain L [auth A] Focus chain R [auth B] Interactions & Density Focus chain L [auth A] Focus chain R [auth B]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B]	K [auth A] M [auth A] N [auth A] Q [auth B] S [auth B] K [auth A], M [auth A], N [auth A], Q [auth B], S [auth B], T [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain Q [auth B] Focus chain S [auth B] Focus chain T [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	O [auth A], P [auth A], U [auth B], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain U [auth B] Focus chain V [auth B]