6YP9 | pdb_00006yp9

Rabbit muscle actin in complex with ADF-H and ATP-ATTO-488

• PDB DOI: https://doi.org/10.2210/pdb6YP9/pdb

• Classification: PROTEIN BINDING
• Organism(s): Oryctolagus cuniculus, Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-04-15 Released: 2020-12-09 
• Deposition Author(s): Kogan, K., Kotila, T., Lappalainen, P.
• Funding Organization(s): Academy of Finland

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free: 
  0.230 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.174 (Depositor) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

Literature

A functional family of fluorescent nucleotide analogues to investigate actin dynamics and energetics.

Colombo, J., Antkowiak, A., Kogan, K., Kotila, T., Elliott, J., Guillotin, A., Lappalainen, P., Michelot, A.

(2021) Nat Commun 12: 548-548

• PubMed: 33483497 
• DOI: https://doi.org/10.1038/s41467-020-20827-4
• Primary Citation Related Structures: 
  6YP9


• PubMed Abstract: 
  

  Actin polymerization provides force for vital processes of the eukaryotic cell, but our understanding of actin dynamics and energetics remains limited due to the lack of high-quality probes. Most current probes affect dynamics of actin or its interactions with actin-binding proteins (ABPs), and cannot track the bound nucleotide. Here, we identify a family of highly sensitive fluorescent nucleotide analogues structurally compatible with actin. We demonstrate that these fluorescent nucleotides bind to actin, maintain functional interactions with a number of essential ABPs, are hydrolyzed within actin filaments, and provide energy to power actin-based processes. These probes also enable monitoring actin assembly and nucleotide exchange with single-molecule microscopy and fluorescence anisotropy kinetics, therefore providing robust and highly versatile tools to study actin dynamics and functions of ABPs.

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Organizational Affiliation: 
• Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, 13288, Marseille, France.
HiLIFE Institute of Biotechnology, P.O. Box 56, University of Helsinki, 00014, Helsinki, Finland.
Aix Marseille Univ, CNRS, IBDM, Turing Centre for Living Systems, 13288, Marseille, France. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 58.86 kDa 
• Atom Count: 4,271 
• Modeled Residue Count: 502 
• Deposited Residue Count: 515 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A	375	Oryctolagus cuniculus	Mutation(s): 0  EC: 3.6.4
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Twinfilin-1	B	140	Mus musculus	Mutation(s): 0  Gene Names: Twf1, Ptk9
UniProt & NIH Common Fund Data Resources
Find proteins for Q91YR1 (Mus musculus) Explore Q91YR1  Go to UniProtKB:  Q91YR1
IMPC:  MGI:1100520

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	C [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC	A	L-PEPTIDE LINKING	C7 H11 N3 O2		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.56 Å
• R-Value Free:  0.230 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.174 (Depositor) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.552	α = 90
b = 69.017	β = 90
c = 147.948	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
autoPROC	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-12-09 
Deposition Author(s): Kogan, K., Kotila, T., Lappalainen, P.

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Funding Organization	Location	Grant Number
Academy of Finland	Finland	320161

Revision History  

• Version 1.0: 2020-12-09
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description