3QMZ | pdb_00003qmz

Crystal structure of the cytoplasmic dynein heavy chain motor domain

• PDB DOI: https://doi.org/10.2210/pdb3QMZ/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Saccharomyces cerevisiae, Schistosoma japonicum
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2011-02-07 Released: 2011-03-16 
• Deposition Author(s): Cho, C., Carter, A.P., Jin, L., Vale, R.D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 6.00 Å
• R-Value Free: 
  0.430 (Depositor), 0.433 (DCC) 
• R-Value Work: 
  0.430 (Depositor), 0.441 (DCC) 

Literature

Crystal structure of the dynein motor domain.

Carter, A.P., Cho, C., Jin, L., Vale, R.D.

(2011) Science 331: 1159-1165

• PubMed: 21330489 
• DOI: https://doi.org/10.1126/science.1202393
• Primary Citation Related Structures: 
  3QMZ


• PubMed Abstract: 
  

  Dyneins are microtubule-based motor proteins that power ciliary beating, transport intracellular cargos, and help to construct the mitotic spindle. Evolved from ring-shaped hexameric AAA-family adenosine triphosphatases (ATPases), dynein's large size and complexity have posed challenges for understanding its structure and mechanism. Here, we present a 6 angstrom crystal structure of a functional dimer of two ~300-kilodalton motor domains of yeast cytoplasmic dynein. The structure reveals an unusual asymmetric arrangement of ATPase domains in the ring-shaped motor domain, the manner in which the mechanical element interacts with the ATPase ring, and an unexpected interaction between two coiled coils that create a base for the microtubule binding domain. The arrangement of these elements provides clues as to how adenosine triphosphate-driven conformational changes might be transmitted across the motor domain.

---

Organizational Affiliation: 
• Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California-San Francisco, 600 16th Street, San Francisco, CA 94158, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 622.58 kDa 
• Atom Count: 23,302 
• Modeled Residue Count: 4,704 
• Deposited Residue Count: 5,410 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytoplasmic dynein heavy chain	A, B	2,486	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36022 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36022  Go to UniProtKB:  P36022

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione-S-transferase	C [auth T], D [auth S]	219	Schistosoma japonicum	Mutation(s): 0  EC: 2.5.1.18
UniProt
Find proteins for P08515 (Schistosoma japonicum) Explore P08515  Go to UniProtKB:  P08515

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 6.00 Å
• R-Value Free:  0.430 (Depositor), 0.433 (DCC) 
• R-Value Work:  0.430 (Depositor), 0.441 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 174.08	α = 90
b = 118.921	β = 90.27
c = 200.509	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	model building
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Cho, C., Carter, A.P., Jin, L., Vale, R.D.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-02-29
  Changes: Database references
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references
• Version 1.4: 2026-02-11
  Changes: Data collection, Structure summary