1YV3 | pdb_00001yv3

The structural basis of blebbistatin inhibition and specificity for myosin II

• PDB DOI: https://doi.org/10.2210/pdb1YV3/pdb

• Classification: CONTRACTILE PROTEIN
• Organism(s): Dictyostelium discoideum
• Mutation(s): No 


• Deposited: 2005-02-14 Released: 2005-03-08 
• Deposition Author(s): Allingham, J.S., Smith, R., Rayment, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

The structural basis of blebbistatin inhibition and specificity for myosin II.

Allingham, J.S., Smith, R., Rayment, I.

(2005) Nat Struct Mol Biol 12: 378-379

• PubMed: 15750603 
• DOI: https://doi.org/10.1038/nsmb908
• Primary Citation Related Structures: 
  1YV3


• PubMed Abstract: 
  

  Molecular motors play a central role in cytoskeletal-mediated cellular processes and thus present an excellent target for cellular control by pharmacological agents. Yet very few such compounds have been found. We report here the structure of blebbistatin, which inhibits specific myosin isoforms, bound to the motor domain of Dictyostelium discoideum myosin II. This reveals the structural basis for its specificity and provides insight into the development of new agents.

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Organizational Affiliation: 
• Department of Biochemistry, University of Wisconsin, 433 Babcock Drive, Madison, Wisconsin 53706, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 87.69 kDa 
• Atom Count: 6,219 
• Modeled Residue Count: 703 
• Deposited Residue Count: 762 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Myosin II heavy chain	A	762	Dictyostelium discoideum	Mutation(s): 0
UniProt
Find proteins for P08799 (Dictyostelium discoideum) Explore P08799  Go to UniProtKB:  P08799

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
BIT	F [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
VO4	C [auth A]	VANADATE ION O4 V LSGOVYNHVSXFFJ-UHFFFAOYSA-N
EDO	G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MG	B [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BIT	BindingDB:  1YV3	IC50: 4900 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.106	α = 90
b = 145.77	β = 90
c = 152.912	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-03-08 
Deposition Author(s): Allingham, J.S., Smith, R., Rayment, I.

Revision History  

• Version 1.0: 2005-03-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary