8RTT

Structure of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin.

PDB DOI: https://doi.org/10.2210/pdb8RTT/pdb
EM Map EMD-19496: 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: 3.56 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

Mechanism of formin-mediated processive elongation of actin filaments revealed by cryo-EM

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

To be published.

Macromolecule Content

Total Structure Weight: 268.56 kDa
Atom Count: 18,155
Modelled Residue Count: 2,277
Deposited Residue Count: 2,359
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	375	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:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Cell division control protein 12	E, I [auth F]	419	Schizosaccharomyces pombe	Mutation(s): 0 Gene Names: cdc12, SPAC1F5.04c
UniProt
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 Group	Q10059
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 H], G [auth I], 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 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]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-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]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C]	L [auth A], O [auth B], R [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Interactions & Density Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-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]

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 H], G [auth I], H [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 H], G [auth I], H [auth J]	Phalloidin	Peptide-like / Toxin		Interactions Focus chain F [auth H] Focus chain G [auth I] Focus chain H [auth J] Interactions & Density Focus chain F [auth H] Focus chain G [auth I] Focus chain H [auth J]