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Cryo-EM structure of phalloidin-stabilized F-actin (aged)

Analyse Cryo-EM structure of phalloidin-stabilized F-actin (aged) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6T20
Type: protein
Length: 1,890 residues
Chains: 10
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Actin, alpha skeletal muscle; Phalloidin
UniProt: P68135
Ligands: ADP, MG
Pockets: 18 · best druggability 0.84

Structure

electron microscopy · 2 distinct chains · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E	Actin, alpha skeletal muscle	protein	371	44% helix, 19% strand	P68135
F, G, H, I, J	Phalloidin	protein	7	0% helix, 0% strand	—

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1129	0.84	0.85	94	empty
2	687	0.83	0.87	77	empty
3	402	0.79	0.88	47	empty
4	250	0.77	0.90	48	ADP, MG
5	276	0.76	0.89	50	ADP, MG

Interfaces

20 interfaces between chains.

B–D · 1173 Å² buried · 11 hydrogen bonds · protein-protein
A–C · 1171 Å² buried · 11 hydrogen bonds · protein-protein
C–E · 1170 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 484 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 482 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 15 modified, 5 d-amino (D-amino acid, hydroxylation, methylation, nonstandard).

Compared structures

6T20 · Cryo-EM structure of phalloidin-stabilized F-actin (aged) · the same entry in another collection · chain J against J, TM-score 1.00
P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain A against A, TM-score 0.96

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P68135
Elsewhere: RCSB PDB 6T20 · PDBe 6T20 · UniProt P68135

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