9FJM

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

PDB DOI: https://doi.org/10.2210/pdb9FJM/pdb
EM Map EMD-50506: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens, Amanita phalloides
Expression System: Trichoplusia ni
Mutation(s): Yes

Deposited: 2024-05-31 Released: 2024-09-11
Deposition Author(s): Boiero Sanders, M., Oosterheert, W., Hofnagel, O., Bieling, P., Raunser, S.
Funding Organization(s): Alexander von Humboldt Foundation, German Research Foundation (DFG), European Research Council (ERC)

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

This is version 1.0 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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, cytoplasmic 1, N-terminally processed	A, B, C, D	374	Homo sapiens	Mutation(s): 1 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60709
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phalloidin	E [auth H], F [auth I], G [auth K], H [auth J]	7	Amanita phalloides	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D]	I [auth A], L [auth B], O [auth C], R [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D]	K [auth A], N [auth B], Q [auth C], T [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain K [auth A] Focus chain N [auth B] Focus chain Q [auth C] Focus chain T [auth D]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth C] SDF format, chain S [auth D] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth C] MOL2 format, chain S [auth D]	J [auth A], M [auth B], P [auth C], S [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain S [auth D]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A, B, C, D	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
HYP Query on HYP	E [auth H], F [auth I], G [auth K], H [auth J]	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002366 Query on PRD_002366	E [auth H], F [auth I], G [auth J], H [auth K]	Phalloidin	Peptide-like / Toxin		Interactions Focus chain E [auth H] Focus chain F [auth I] Focus chain G [auth K] Focus chain H [auth J] Interactions & Density Focus chain E [auth H] Focus chain F [auth I] Focus chain G [auth K] Focus chain H [auth J]