8R3H | pdb_00008r3h

Phalloidin bound F-actin

PDB DOI: https://doi.org/10.2210/pdb8R3H/pdb
EM Map EMD-18866: EMDB EMDataResource

Classification: CYTOSOLIC PROTEIN
Organism(s): Gallus, Amanita phalloides
Expression System: Gallus
Mutation(s): No

Deposited: 2023-11-09 Released: 2025-05-21
Deposition Author(s): Yuan, B., Paraschiakos, T., Windhorst, S., Marlovits, T.C.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

wwPDB Validation 3D Report Full Report

Validation slider image for 8R3H

This is version 1.0 of the entry. See complete history.

Literature

Phalloidin bound F-actin

Yuan, B., Paraschiakos, T., Windhorst, S., Marlovits, T.C.

To be published.

Macromolecule Content

Total Structure Weight: 215.23 kDa
Atom Count: 14,670
Modeled Residue Count: 1,861
Deposited Residue Count: 1,906
Unique protein chains: 2

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A [auth F], B [auth G], C [auth H], D [auth I], E [auth J]	377	Gallus	Mutation(s): 0 Gene Names: ACTA1, ACTA EC: 3.6.4
UniProt
Find proteins for P68139 (Gallus gallus) Explore P68139 Go to UniProtKB: P68139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68139
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
phalloidin	F [auth X], G [auth Y], H [auth Z]	7	Amanita phalloides	Mutation(s): 0

Small Molecules

Ligands 2 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 R [auth J] SDF format, chain P [auth I] SDF format, chain N [auth H] SDF format, chain L [auth G] SDF format, chain J [auth F] MOL2 format, chain R [auth J] MOL2 format, chain P [auth I] MOL2 format, chain N [auth H] MOL2 format, chain L [auth G] MOL2 format, chain J [auth F] mmCIF format, chain R [auth J] mmCIF format, chain P [auth I] mmCIF format, chain N [auth H] mmCIF format, chain L [auth G] mmCIF format, chain J [auth F]	J [auth F], L [auth G], N [auth H], P [auth I], R [auth J]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain J [auth F] Focus chain L [auth G] Focus chain N [auth H] Focus chain P [auth I] Focus chain R [auth J] Interactions & Density Focus chain J [auth F] Focus chain L [auth G] Focus chain N [auth H] Focus chain P [auth I] Focus chain R [auth J]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth J] SDF format, chain O [auth I] SDF format, chain M [auth H] SDF format, chain K [auth G] SDF format, chain I [auth F] MOL2 format, chain Q [auth J] MOL2 format, chain O [auth I] MOL2 format, chain M [auth H] MOL2 format, chain K [auth G] MOL2 format, chain I [auth F] mmCIF format, chain Q [auth J] mmCIF format, chain O [auth I] mmCIF format, chain M [auth H] mmCIF format, chain K [auth G] mmCIF format, chain I [auth F]	I [auth F], K [auth G], M [auth H], O [auth I], Q [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain I [auth F] Focus chain K [auth G] Focus chain M [auth H] Focus chain O [auth I] Focus chain Q [auth J] Interactions & Density Focus chain I [auth F] Focus chain K [auth G] Focus chain M [auth H] Focus chain O [auth I] Focus chain Q [auth J]

Modified Residues 4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIC Query on HIC	A [auth F], B [auth G], C [auth H], D [auth I], E [auth J]	L-PEPTIDE LINKING	C₇ H₁₁ N₃ O₂		HIS
ALO Query on ALO	F [auth X], G [auth Y], H [auth Z]	L-PEPTIDE LINKING	C₄ H₉ N O₃		THR
G5G Query on G5G	F [auth X], G [auth Y], H [auth Z]	L-PEPTIDE LINKING	C₆ H₁₃ N O₄		LEU
HYP Query on HYP	F [auth X], G [auth Y], H [auth Z]	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: FILAMENT
Reconstruction Method: HELICAL

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-05-21

Deposition Author(s):

Paraschiakos, T.

Marlovits, T.C.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	152/774-1, 152/775-1, 152/776-1 and 152/777-1

Revision History (Full details and data files)

Version 1.0: 2025-05-21
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.