6FM2

CARP domain of mouse cyclase-associated protein 1 (CAP1) bound to ADP-actin

• PDB DOI:  https://doi.org/10.2210/pdb6FM2/pdb

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


• Deposited: 2018-01-30 Released: 2018-05-16 
• Deposition Author(s): Kotila, T.M., Kogan, K., Lappalainen, P.
• Funding Organization(s): Academy of Finland, European Research Council, National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI), National Science Foundation (United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 

Literature

Structural basis of actin monomer re-charging by cyclase-associated protein.

Kotila, T., Kogan, K., Enkavi, G., Guo, S., Vattulainen, I., Goode, B.L., Lappalainen, P.

(2018) Nat Commun 9: 1892-1892

• PubMed: 29760438 
• DOI: https://doi.org/10.1038/s41467-018-04231-7
• Primary Citation of Related Structures:  
  6FM2


• PubMed Abstract: 
  

Actin polymerization powers key cellular processes, including motility, morphogenesis, and endocytosis. The actin turnover cycle depends critically on "re-charging" of ADP-actin monomers with ATP, but whether this reaction requires dedicated proteins in cells, and the underlying mechanism, have remained elusive. Here we report that nucleotide exchange catalyzed by the ubiquitous cytoskeletal regulator cyclase-associated protein (CAP) is critical for actin-based processes in vivo. We determine the structure of the CAP-actin complex, which reveals that nucleotide exchange occurs in a compact, sandwich-like complex formed between the dimeric actin-binding domain of CAP and two ADP-actin monomers. In the crystal structure, the C-terminal tail of CAP associates with the nucleotide-sensing region of actin, and this interaction is required for rapid re-charging of actin by both yeast and mammalian CAPs. These data uncover the conserved structural basis and biological role of protein-catalyzed re-charging of actin monomers.

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Organizational Affiliation: 

Institute of Biotechnology, University of Helsinki, 00014, Helsinki, Finland. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 59.85 kDa 
• Atom Count: 4,228 
• Modelled Residue Count: 528 
• Deposited Residue Count: 533 
• 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  Gene Names: ACTA1, ACTA
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135  Go to UniProtKB:  P68135

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylyl cyclase-associated protein 1	B	158	Mus musculus	Mutation(s): 0  Gene Names: Cap1, Cap
UniProt
Find proteins for P40124 (Mus musculus) Explore P40124  Go to UniProtKB:  P40124

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP (Subject of Investigation/LOI)	D [auth A]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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: 2.80 Å
• R-Value Free: 0.234 
• R-Value Work: 0.183 
• R-Value Observed: 0.186 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.833	α = 90
b = 73.833	β = 90
c = 453.377	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
BALBES	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-16 
Deposition Author(s): Kotila, T.M., Kogan, K., Lappalainen, P.

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Funding Organization	Location	Grant Number
Academy of Finland	Finland	272130
Academy of Finland	Finland	307415
European Research Council	Finland	290974
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	R01 GM063691
National Science Foundation (United States)	United States	DMR-1420382

Revision History  

• Version 1.0: 2018-05-16
  Type: Initial release
  
• Version 1.1: 2018-05-23
  Changes: Data collection, Database references
• Version 1.2: 2022-03-30
  Changes: Author supporting evidence, Database references, Derived calculations