8OID

Cryo-EM structure of ADP-bound, filamentous beta-actin harboring the N111S mutation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular mechanisms of inorganic-phosphate release from the core and barbed end of actin filaments.

Oosterheert, W.Blanc, F.E.C.Roy, A.Belyy, A.Sanders, M.B.Hofnagel, O.Hummer, G.Bieling, P.Raunser, S.

(2023) Nat Struct Mol Biol 30: 1774-1785

  • DOI: https://doi.org/10.1038/s41594-023-01101-9
  • Primary Citation of Related Structures:  
    8OI6, 8OI8, 8OID

  • PubMed Abstract: 

    The release of inorganic phosphate (P i ) from actin filaments constitutes a key step in their regulated turnover, which is fundamental to many cellular functions. The mechanisms underlying P i release from the core and barbed end of actin filaments remain unclear. Here, using human and bovine actin isoforms, we combine cryo-EM with molecular-dynamics simulations and in vitro reconstitution to demonstrate how actin releases P i through a 'molecular backdoor'. While constantly open at the barbed end, the backdoor is predominantly closed in filament-core subunits and opens only transiently through concerted amino acid rearrangements. This explains why P i escapes rapidly from the filament end but slowly from internal subunits. In a nemaline-myopathy-associated actin variant, the backdoor is predominantly open in filament-core subunits, resulting in accelerated P i release and filaments with drastically shortened ADP-P i caps. Our results provide the molecular basis for P i release from actin and exemplify how a disease-linked mutation distorts the nucleotide-state distribution and atomic structure of the filament.


  • Organizational Affiliation

    Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1, N-terminally processedA [auth C],
B [auth A],
C [auth B],
D,
E
375Homo sapiensMutation(s): 2 
Gene Names: ACTB
UniProt & NIH Common Fund Data Resources
Find proteins for P60709 (Homo sapiens)
Explore P60709 
Go to UniProtKB:  P60709
PHAROS:  P60709
GTEx:  ENSG00000075624 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60709
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
F [auth C],
H [auth A],
J [auth B],
L [auth D],
N [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
G [auth C],
I [auth A],
K [auth B],
M [auth D],
O [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
A [auth C],
B [auth A],
C [auth B],
D,
E
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.0
MODEL REFINEMENTPHENIX1.20.1-4487-000

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
Alexander von Humboldt FoundationGermany--
European Research Council (ERC)European Union856118

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2023-09-27
    Changes: Database references, Refinement description
  • Version 1.3: 2023-10-04
    Changes: Database references
  • Version 1.4: 2023-11-22
    Changes: Database references