9GKP | pdb_00009gkp

Structure of fragacetoxin C in lipid nanodiscs


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Elucidating the structure and assembly mechanism of actinoporin pores in complex membrane environments.

Arranz, R.Santiago, C.Masiulis, S.Rivera-de-Torre, E.Palacios-Ortega, J.Carlero, D.Heras-Marquez, D.Gavilanes, J.G.Arias-Palomo, E.Martinez-Del-Pozo, A.Garcia-Linares, S.Martin-Benito, J.

(2025) Sci Adv 11: eadv0683-eadv0683

  • DOI: https://doi.org/10.1126/sciadv.adv0683
  • Primary Citation of Related Structures:  
    9GJ8, 9GKI, 9GKL, 9GKO, 9GKP

  • PubMed Abstract: 

    Pore-forming proteins exemplify the transformative potential of biological molecules. Produced as soluble monomers, they assemble into multimeric membrane-inserted complexes in response to specific membrane environments. Actinoporins, a class of pore-forming proteins from sea anemones, target membranes to kill cells. Here, we report cryogenic electron microscopy structures of two actinoporins, fragaceatoxin C and sticholysin II, reconstituted in lipid membranes. The structures reveal an ordered arrangement of dozens of lipid molecules that form an integral part of the pore architecture. We also captured distinct oligomeric intermediates, arc-shaped assemblies with monomers in transitional conformations, representing key snapshots along the pore formation pathway. These data provide direct structural evidence for a stepwise mechanism in which monomers sequentially bind the membrane and undergo conformational changes that drive pore assembly and membrane disruption. Our findings reveal how these proteins reshape membranes and offer mechanistic insights into their cytolytic activity. This work broadens our understanding of pore-forming proteins, which are gaining increasing relevance in diverse biotechnological applications.


  • Organizational Affiliation
    • Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Calle Darwin 3, 28049 Madrid, Spain.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DELTA-actitoxin-Afr1a178Actinia fragaceaMutation(s): 0 
UniProt
Find proteins for B9W5G6 (Actinia fragacea)
Explore B9W5G6 
Go to UniProtKB:  B9W5G6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9W5G6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FO4 (Subject of Investigation/LOI)
Query on FO4

Download Ideal Coordinates CCD File 
AC [auth E]
BC [auth E]
CC [auth F]
DB [auth C]
DC [auth F]
AC [auth E],
BC [auth E],
CC [auth F],
DB [auth C],
DC [auth F],
EA [auth A],
EB [auth D],
EC [auth F],
FA [auth A],
FB [auth D],
FC [auth F],
GA [auth B],
GB [auth D],
GC [auth F],
HA [auth B],
HB [auth D],
HC [auth F],
I [auth G],
IA [auth B],
IB [auth D],
J [auth G],
JA [auth B],
JB [auth D],
K [auth G],
KA [auth B],
L [auth G],
LA [auth B],
MC [auth F],
NC [auth F],
OB [auth D],
OC [auth H],
PB [auth D],
PC [auth H],
Q [auth G],
QA [auth B],
QB [auth E],
QC [auth H],
R [auth G],
RA [auth B],
RB [auth E],
RC [auth H],
S [auth G],
SA [auth B],
SB [auth E],
SC [auth H],
T [auth G],
TA [auth C],
TB [auth E],
TC [auth H],
U [auth A],
UA [auth C],
UB [auth E],
V [auth A],
VA [auth C],
VB [auth E],
W [auth A],
WA [auth C],
X [auth A],
XA [auth C],
Y [auth A],
YA [auth C],
YC [auth H],
Z [auth A],
ZC [auth H]
sphingomyelin
C47 H94 N2 O6 P
NHYQHBPEJLFFSO-QYKFWSDSSA-O
CLR (Subject of Investigation/LOI)
Query on CLR

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth C]
BA [auth A]
BB [auth C]
CA [auth A]
AA [auth A],
AB [auth C],
BA [auth A],
BB [auth C],
CA [auth A],
CB [auth C],
DA [auth A],
IC [auth F],
JC [auth F],
KB [auth D],
KC [auth F],
LB [auth D],
LC [auth F],
M [auth G],
MA [auth B],
MB [auth D],
N [auth G],
NA [auth B],
NB [auth D],
O [auth G],
OA [auth B],
P [auth G],
PA [auth B],
UC [auth H],
VC [auth H],
WB [auth E],
WC [auth H],
XB [auth E],
XC [auth H],
YB [auth E],
ZA [auth C],
ZB [auth E]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-117752RB-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainTED2021-132748B-I00
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2024-162190OB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release