Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 394.92 kDa 
• Atom Count: 22816 
• Modelled Residue Count: 3005 
• Deposited Residue Count: 3450 
• Unique protein chains: 1

4RH7

Crystal structure of human cytoplasmic dynein 2 motor domain in complex with ADP.Vi

• PDB DOI: 10.2210/pdb4RH7/pdb

• Classification: MOTOR PROTEIN
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2014-10-01 Released: 2014-12-10 
• Deposition Author(s): Schmidt, H., Zalyte, R., Urnavicius, L., Carter, A.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free: 0.285 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 

Literature

Structure of human cytoplasmic dynein-2 primed for its power stroke.

Schmidt, H., Zalyte, R., Urnavicius, L., Carter, A.P.

(2015) Nature 518: 435-438

• PubMed: 25470043 
• DOI: 10.1038/nature14023
• Primary Citation of Related Structures:  
  4RH7


• PubMed Abstract: 
  

Members of the dynein family, consisting of cytoplasmic and axonemal isoforms, are motors that move towards the minus ends of microtubules. Cytoplasmic dynein-1 (dynein-1) plays roles in mitosis and cellular cargo transport, and is implicated in viral infections and neurodegenerative diseases. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Here we present the crystal structure of the human cytoplasmic dynein-2 motor bound to the ATP-hydrolysis transition state analogue ADP.vanadate. The structure reveals a closure of the motor's ring of six AAA+ domains (ATPases associated with various cellular activites: AAA1-AAA6). This induces a steric clash with the linker, the key element for the generation of movement, driving it into a conformation that is primed to produce force. Ring closure also changes the interface between the stalk and buttress coiled-coil extensions of the motor domain. This drives helix sliding in the stalk which causes the microtubule binding domain at its tip to release from the microtubule. Our structure answers the key questions of how ATP hydrolysis leads to linker remodelling and microtubule affinity regulation.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Division of Structural Studies, Francis Crick Avenue, Cambridge, CB2 0QH, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Green fluorescent protein/Cytoplasmic dynein 2 heavy chain 1	A	3450	synthetic construct, Homo sapiens This entity is chimeric	Mutation(s): 3
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NCM8 (Homo sapiens) Explore Q8NCM8  Go to UniProtKB:  Q8NCM8
PHAROS:  Q8NCM8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AOV	B [auth A]	ADP ORTHOVANADATE C10 H17 N5 O14 P2 V SWCHWRVRYDCWAN-AZGWGOJFSA-J
ATP	D [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP	F [auth A], G [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG	C [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.41 Å
• R-Value Free: 0.285 
• R-Value Work: 0.237 
• R-Value Observed: 0.240 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.03	α = 90
b = 487.15	β = 90
c = 276.46	γ = 90

Software Package:

Software Name	Purpose
SHARP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-10-01 
• Released Date: 2014-12-10 
Deposition Author(s): Schmidt, H., Zalyte, R., Urnavicius, L., Carter, A.P.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2015-04-08
  Changes: Database references
• Version 1.3: 2017-08-02
  Changes: Refinement description, Source and taxonomy