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

Structure

electron microscopy · 1 distinct chain · 45% helix, 20% strand (DSSP).

Ligands and binding sites

• ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E
• 9ZK · (4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-10-(4-azanylbutyl)-4-(4-hydroxyphenyl)-7-(1~{H}-indol-3-ylmethyl)-8,13,15,19-tetramethyl-1-oxa-5,8,11-triazacyclononadec-15-ene-2,6,9,12-tetrone · ligand · 5 copies · chains A, B, C, D, E
• MG · Magnesium ion · metal · 5 copies · chains A, B, C, D, E
• PO4 · Phosphate ion · ion · 5 copies · chains A, B, C, D, E

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

Pockets

16 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.

Interfaces

7 interfaces between chains.

• C–E · 1083 Ų buried · 12 hydrogen bonds · protein-protein
• A–C · 1081 Ų buried · 12 hydrogen bonds · protein-protein
• B–D · 1077 Ų buried · 12 hydrogen bonds · protein-protein
• C–D · 531 Ų buried · 7 hydrogen bonds · protein-protein
• B–C · 525 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 modified (methylation).

Compared structures

• 6T23 · Cryo-EM structure of jasplakinolide-stabilized F-actin (aged) · the same entry in another collection · chain E against E, TM-score 1.00
• P68135 · AlphaFold monomer V2.0 prediction for actin, alpha skeletal muscle (P68135) · a predicted model of the same protein · chain D against A, TM-score 0.95

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 6T23 · PDBe 6T23 · UniProt P68135