9FJY

Structure of the DNase I- and phalloidin-bound pointed end of F-actin (conformer 2).

PDB DOI: https://doi.org/10.2210/pdb9FJY/pdb
EM Map EMD-50517: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Bos taurus, Amanita phalloides
Mutation(s): No

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: 3.79 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
View more details

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: 235.77 kDa
Atom Count: 15,968
Modelled Residue Count: 2,014
Deposited Residue Count: 2,088
Unique protein chains: 3

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	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P60712 (Bos taurus) Explore P60712 Go to UniProtKB: P60712
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60712
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyribonuclease-1	E, J [auth F]	282	Bos taurus	Mutation(s): 0 EC: 3.1.21.1
UniProt
Find proteins for P00639 (Bos taurus) Explore P00639 Go to UniProtKB: P00639
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00639
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E Focus chain J [auth F]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Phalloidin	F [auth G], G [auth H], H [auth I], I [auth J]	7	Amanita phalloides	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L	2		N-Glycosylation	Interactions Focus chain K Focus chain L Interactions & Density Focus chain K Focus chain L

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 M [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D]	M [auth A], P [auth B], S [auth C], V [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain U [auth C] SDF format, chain X [auth D] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth D]	O [auth A], R [auth B], U [auth C], X [auth D]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth D] Interactions & Density Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C] Focus chain X [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain Y [auth E] SDF format, chain Z [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E]	AA [auth F] BA [auth F] N [auth A] Q [auth B] T [auth C] AA [auth F], BA [auth F], N [auth A], Q [auth B], T [auth C], W [auth D], Y [auth E], Z [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Y [auth E] Focus chain Z [auth E]

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	F [auth G], G [auth H], H [auth I], I [auth J]	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO

Biologically Interesting Molecules (External Reference) 1 Unique

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