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 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of Pre-Chi dynein bound to Lis1

Nguyen, K.H.V., Kendrick, A.A., Leschziner, A.E.

To be published.

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

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, 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	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 L [auth B] SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] 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 N [auth B] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	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

View Full Validation Report

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