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 8OI6 | pdb_00008oi6

Cryo-EM structure of the undecorated barbed end of filamentous beta/gamma actin


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8OI6

This is version 1.5 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 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.

Macromolecule Content 

  • Total Structure Weight: 171.42 kDa 
  • Atom Count: 11,573 
  • Modeled Residue Count: 1,467 
  • Deposited Residue Count: 1,521 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1
A, B, C, D
375Bos taurusMutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for P60712 (Bos taurus)
Explore P60712 
Go to UniProtKB:  P60712
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60712
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PHALLOIDINE [auth H],
F [auth I],
G [auth J]
7Amanita phalloidesMutation(s): 0 
Sequence Annotations
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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
H [auth A],
J [auth B],
L [auth C],
N [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
I [auth A],
K [auth B],
M [auth C],
O [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  4 Unique
IDChains TypeFormula2D DiagramParent
HIC
Query on HIC
A, B, C, D
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
DTH
Query on DTH
E [auth H],
F [auth I],
G [auth J]
D-PEPTIDE LINKINGC4 H9 N O3

--

EEP
Query on EEP
E [auth H],
F [auth I],
G [auth J]
L-PEPTIDE LINKINGC6 H13 N O4

--

HYP
Query on HYP
E [auth H],
F [auth I],
G [auth J]
L-PEPTIDE LINKINGC5 H9 N O3PRO

Biologically Interesting Molecules (External Reference) 

1 Unique

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487-000
RECONSTRUCTIONcryoSPARC3.3.2

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
  • Version 1.2: 2023-09-27
    Changes: Database references, Refinement description
  • Version 1.3: 2023-10-04
    Changes: Database references
  • Version 1.4: 2023-11-15
    Changes: Data collection
  • Version 1.5: 2023-11-22
    Changes: Database references