8RTY

Structure of the F-actin barbed end bound by Cdc12 and profilin (ring complex) at a resolution of 6.3 Angstrom

PDB DOI: https://doi.org/10.2210/pdb8RTY/pdb
EM Map EMD-19499: EMDB EMDataResource

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

Deposited: 2024-01-29 Released: 2024-04-10
Deposition Author(s): Oosterheert, W., Boiero Sanders, M., Funk, J., Prumbaum, D., Raunser, S., Bieling, P.
Funding Organization(s): Alexander von Humboldt Foundation, German Research Foundation (DFG), European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 6.25 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Molecular mechanism of actin filament elongation by formins.

Oosterheert, W., Boiero Sanders, M., Funk, J., Prumbaum, D., Raunser, S., Bieling, P.

(2024) Science 384: eadn9560-eadn9560

PubMed: 38603491 Search on PubMed
DOI: https://doi.org/10.1126/science.adn9560
Primary Citation of Related Structures:
8RTY, 8RU0, 8RU2, 8RV2

PubMed Abstract:
Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action remain unclear. In this work, we present high-resolution cryo-electron microscopy structures of F-actin barbed ends bound by three distinct formins, revealing a common asymmetric formin conformation imposed by the filament. Formation of new intersubunit contacts during actin polymerization sterically displaces formin and triggers its translocation. This "undock-and-lock" mechanism explains how actin-filament growth is coordinated with formin movement. Filament elongation speeds are controlled by the positioning and stability of actin-formin interfaces, which distinguish fast and slow formins. Furthermore, we provide a structure of the actin-formin-profilin ring complex, which resolves how profilin is rapidly released from the barbed end during filament elongation.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 341.83 kDa
Atom Count: 19,260
Modelled Residue Count: 2,424
Deposited Residue Count: 3,062
Unique protein chains: 4

Macromolecules

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(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

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylated-DNA--protein-cysteine methyltransferase,Cell division control protein 12	E, F	703	Homo sapiens, Schizosaccharomyces pombe This entity is chimeric	Mutation(s): 11 Gene Names: MGMT, cdc12, SPAC1F5.04c EC: 2.1.1.63
UniProt & NIH Common Fund Data Resources
Find proteins for P16455 (Homo sapiens) Explore P16455 Go to UniProtKB: P16455
PHAROS: P16455 GTEx: ENSG00000170430
Find proteins for Q10059 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore Q10059 Go to UniProtKB: Q10059
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P16455Q10059
Sequence Annotations Expand
Reference Sequence

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

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Profilin-1	J [auth P]	139	Homo sapiens	Mutation(s): 2 Gene Names: PFN1
UniProt & NIH Common Fund Data Resources
Find proteins for P07737 (Homo sapiens) Explore P07737 Go to UniProtKB: P07737
PHAROS: P07737 GTEx: ENSG00000108518
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07737
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 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]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		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]
PO4 (Subject of Investigation/LOI) Query on PO4 Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C]	M [auth A], P [auth B], S [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Interactions & Density Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D]	L [auth A], O [auth B], R [auth C], U [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [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	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	G [auth H], H [auth I], I [auth J]	Phalloidin	Peptide-like / Toxin		Interactions Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J] Interactions & Density Focus chain G [auth H] Focus chain H [auth I] Focus chain I [auth J]