9FJM | pdb_00009fjm

Cryo-EM structure of the phalloidin-bound pointed end of the actin filament.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 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 9FJM

This is version 1.1 of the entry. See complete history

Literature

Phalloidin and DNase I-bound F-actin pointed end structures reveal principles of filament stabilization and disassembly.

Boiero Sanders, M.Oosterheert, W.Hofnagel, O.Bieling, P.Raunser, S.

(2024) Nat Commun 15: 7969-7969

  • DOI: https://doi.org/10.1038/s41467-024-52251-3
  • Primary Citation Related Structures: 
    9FJM, 9FJO, 9FJU, 9FJY

  • PubMed Abstract: 

    Actin filament turnover involves subunits binding to and dissociating from the filament ends, with the pointed end being the primary site of filament disassembly. Several molecules modulate filament turnover, but the underlying mechanisms remain incompletely understood. Here, we present three cryo-EM structures of the F-actin pointed end in the presence and absence of phalloidin or DNase I. The two terminal subunits at the undecorated pointed end adopt a twisted conformation. Phalloidin can still bind and bridge these subunits, inducing a conformational shift to a flattened, F-actin-like state. This explains how phalloidin prevents depolymerization at the pointed end. Interestingly, two DNase I molecules simultaneously bind to the phalloidin-stabilized pointed end. In the absence of phalloidin, DNase I binding would disrupt the terminal actin subunit packing, resulting in filament disassembly. Our findings uncover molecular principles of pointed end regulation and provide structural insights into the kinetic asymmetry between the actin filament ends.


  • Organizational Affiliation
    • Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany.

Macromolecule Content 

  • Total Structure Weight: 171.95 kDa 
  • Atom Count: 11,772 
  • Modeled Residue Count: 1,491 
  • Deposited Residue Count: 1,524 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin, cytoplasmic 1, N-terminally processed
A, B, C, D
374Homo sapiensMutation(s): 1 
Gene Names: ACTB
EC: 3.6.4
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
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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 K],
H [auth J]
7Amanita phalloidesMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
I [auth A],
L [auth B],
O [auth C],
R [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
PO4
(Subject of Investigation/LOI)

Query on PO4



Download:Ideal Coordinates CCD File
K [auth A],
N [auth B],
Q [auth C],
T [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
J [auth A],
M [auth B],
P [auth C],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 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 K],
H [auth J]
D-PEPTIDE LINKINGC4 H9 N O3

--

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

--

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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.65 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARCv4.2.1
MODEL REFINEMENTCoot0.9.8.1
MODEL REFINEMENTPHENIX1.21rc1_5015

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Alexander von Humboldt FoundationGermany--
German Research Foundation (DFG)GermanyBI 1998/2-1
European Research Council (ERC)European Union856118

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Data collection, Database references