5O2L | pdb_00005o2l

Myosin VI motor domain in the Pre-Transition State

• PDB DOI: https://doi.org/10.2210/pdb5O2L/pdb

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


• Deposited: 2017-05-22 Released: 2018-05-23 
• Deposition Author(s): Isabet, T., Benisty, H., Houdusse, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.182 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

An intermediate along the recovery stroke of myosin VI revealed by X-ray crystallography and molecular dynamics.

Blanc, F., Isabet, T., Benisty, H., Sweeney, H.L., Cecchini, M., Houdusse, A.

(2018) Proc Natl Acad Sci U S A 115: 6213-6218

• PubMed: 29844196 
• DOI: https://doi.org/10.1073/pnas.1711512115
• Primary Citation Related Structures: 
  5O2L


• PubMed Abstract: 
  

  Myosins form a class of actin-based, ATPase motor proteins that mediate important cellular functions such as cargo transport and cell motility. Their functional cycle involves two large-scale swings of the lever arm: the force-generating powerstroke, which takes place on actin, and the recovery stroke during which the lever arm is reprimed into an armed configuration. Previous analyses of the prerecovery (postrigor) and postrecovery (prepowerstroke) states predicted that closure of switch II in the ATP binding site precedes the movement of the converter and the lever arm. Here, we report on a crystal structure of myosin VI, called pretransition state (PTS), which was solved at 2.2 Å resolution. Structural analysis and all-atom molecular dynamics simulations are consistent with PTS being an intermediate along the recovery stroke, where the Relay/SH1 elements adopt a postrecovery conformation, and switch II remains open. In this state, the converter appears to be largely uncoupled from the motor domain and explores an ensemble of partially reprimed configurations through extensive, reversible fluctuations. Moreover, we found that the free energy cost of hydrogen-bonding switch II to ATP is lowered by more than 10 kcal/mol compared with the prerecovery state. These results support the conclusion that closing of switch II does not initiate the recovery stroke transition in myosin VI. Rather, they suggest a mechanism in which lever arm repriming would be mostly driven by thermal fluctuations and eventually stabilized by the switch II interaction with the nucleotide in a ratchet-like fashion.

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Organizational Affiliation: 
• Structural Motility, Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR 144, F-75005 Paris, France.
Sorbonne Universités, Université Pierre et Marie Curie (UPMC) University Paris 06, CNRS, UMR 144, F-75005 Paris, France.
Institut de Science et d'Ingénierie Supramoléculaires (ISIS), UMR 7006 CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France.
Institut de Chimie de Strasbourg, UMR 7177 CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France.
Department of Pharmacology & Therapeutics, University of Florida College of Medicine, Gainesville, FL 32610-0267.
Myology Institute, University of Florida College of Medicine, Gainesville, FL 32610-0267.
Institut de Science et d'Ingénierie Supramoléculaires (ISIS), UMR 7006 CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France; [e-mail] [e-mail].
Structural Motility, Institut Curie, Paris Sciences et Lettres (PSL) Research University, CNRS, UMR 144, F-75005 Paris, France; [e-mail] [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 90.8 kDa 
• Atom Count: 6,387 
• Modeled Residue Count: 763 
• Deposited Residue Count: 785 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Unconventional myosin-VI	A	785	Sus scrofa	Mutation(s): 0  Gene Names: MYO6
UniProt
Find proteins for Q29122 (Sus scrofa) Explore Q29122  Go to UniProtKB:  Q29122

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	B [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
BEF	D [auth A]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.227 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.182 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.34	α = 90
b = 83.83	β = 90
c = 177.66	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
Coot	model building
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Isabet, T., Benisty, H., Houdusse, A.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2018-06-13
  Changes: Data collection, Database references
• Version 1.2: 2018-06-20
  Changes: Data collection, Database references
• Version 1.3: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description