6Z7U | pdb_00006z7u

Myosin-II motor domain complexed with blebbistatin in a new ADP-release conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 
    0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.202 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural and Computational Insights into a Blebbistatin-Bound Myosin•ADP Complex with Characteristics of an ADP-Release Conformation along the Two-Step Myosin Power Stoke.

Ewert, W.Franz, P.Tsiavaliaris, G.Preller, M.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21197417
  • Primary Citation Related Structures: 
    6Z7T, 6Z7U

  • PubMed Abstract: 

    The motor protein myosin drives a wide range of cellular and muscular functions by generating directed movement and force, fueled through adenosine triphosphate (ATP) hydrolysis. Release of the hydrolysis product adenosine diphosphate (ADP) is a fundamental and regulatory process during force production. However, details about the molecular mechanism accompanying ADP release are scarce due to the lack of representative structures. Here we solved a novel blebbistatin-bound myosin conformation with critical structural elements in positions between the myosin pre-power stroke and rigor states. ADP in this structure is repositioned towards the surface by the phosphate-sensing P-loop, and stabilized in a partially unbound conformation via a salt-bridge between Arg131 and Glu187. A 5 Å rotation separates the mechanical converter in this conformation from the rigor position. The crystallized myosin structure thus resembles a conformation towards the end of the two-step power stroke, associated with ADP release. Computationally reconstructing ADP release from myosin by means of molecular dynamics simulations further supported the existence of an equivalent conformation along the power stroke that shows the same major characteristics in the myosin motor domain as the resolved blebbistatin-bound myosin-II·ADP crystal structure, and identified a communication hub centered on Arg232 that mediates chemomechanical energy transduction.


  • Organizational Affiliation
    • Institute for Biophysical Chemistry, Structural Bioinformatics and Chemical Biology, Hannover Medical School, 30625 Hannover, Germany.

Macromolecule Content 

  • Total Structure Weight: 90 kDa 
  • Atom Count: 6,089 
  • Modeled Residue Count: 752 
  • Deposited Residue Count: 777 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Myosin-2 heavy chain777Dictyostelium discoideumMutation(s): 0 
Gene Names: mhcADDB_G0286355
UniProt
Find proteins for P08799 (Dictyostelium discoideum)
Explore P08799 
Go to UniProtKB:  P08799
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08799
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
C [auth A]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BIT
(Subject of Investigation/LOI)

Query on BIT



Download:Ideal Coordinates CCD File
D [auth A](-)-1-PHENYL-1,2,3,4-TETRAHYDRO-4-HYDROXYPYRROLO[2,3-B]-7-METHYLQUINOLIN-4-ONE
C18 H16 N2 O2
LZAXPYOBKSJSEX-GOSISDBHSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
B [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BIT BindingDB:  6Z7U IC50: 4900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.202 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.373α = 90
b = 88.697β = 90
c = 199.891γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyPR 1478/2-1

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-21
    Type: Initial release
  • Version 1.1: 2020-10-28
    Changes: Database references
  • Version 1.2: 2024-01-24
    Changes: Data collection, Database references, Refinement description