7AHQ

Cryo-EM structure of F-actin stabilized by trans-optoJASP-8

PDB DOI: https://doi.org/10.2210/pdb7AHQ/pdb
EM Map EMD-11790: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2020-09-25 Released: 2021-01-27
Deposition Author(s): Pospich, S., Raunser, S.
Funding Organization(s): Max Planck Society, European Union (EU)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: FILAMENT
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Cryo-EM Resolves Molecular Recognition Of An Optojasp Photoswitch Bound To Actin Filaments In Both Switch States.

Pospich, S., Kullmer, F., Nasufovic, V., Funk, J., Belyy, A., Bieling, P., Arndt, H.D., Raunser, S.

(2021) Angew Chem Int Ed Engl 60: 8678-8682

PubMed: 33449370 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/anie.202013193
Primary Citation of Related Structures:
7AHN, 7AHQ

PubMed Abstract:
Actin is essential for key processes in all eukaryotic cells. Cellpermeable optojasps provide spatiotemporal control of the actin cytoskeleton, confining toxicity and potentially rendering F-actin druggable by photopharmacology. Here, we report cryo electron microscopy (cryo-EM) structures of both isomeric states of one optojasp bound to actin filaments. The high-resolution structures reveal for the first time the pronounced effects of photoswitching a functionalized azobenzene. By characterizing the optojasp binding site and identifying conformational changes within F-actin that depend on the optojasp isomeric state, we refine determinants for the design of functional F-actin photoswitches.

Organizational Affiliation

Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.

Macromolecule Content

Total Structure Weight: 218.65 kDa
Atom Count: 15,055
Modelled Residue Count: 1,855
Deposited Residue Count: 1,885
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Actin, alpha skeletal muscle	A, B, C, D, E	377	Oryctolagus cuniculus	Mutation(s): 0
UniProt
Find proteins for P68135 (Oryctolagus cuniculus) Explore P68135 Go to UniProtKB: P68135
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P68135
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RLZ (Subject of Investigation/LOI) Query on RLZ Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain U [auth D] SDF format, chain V [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth E]	I [auth A], M [auth C], Q [auth D], U [auth D], V [auth E]	~{N}-[4-[(4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-4-(4-hydroxyphenyl)-7-(1~{H}-indol-3-ylmethyl)-8,13,15,19-tetramethyl-2,6,9,12-tetrakis(oxidanylidene)-1-oxa-5,8,11-triazacyclononadec-15-en-10-yl]butyl]-~{N}'-[5-methoxy-2-[(~{Z})-(3,4,5-trimethoxyphenyl)diazenyl]phenyl]butanediamide C₅₈ H₇₂ N₈ O₁₂ NHSDRYIAMSCFAB-MHSPIPMPSA-N		Interactions Focus chain I [auth A] Focus chain M [auth C] Focus chain Q [auth D] Focus chain U [auth D] Focus chain V [auth E] Interactions & Density Focus chain I [auth A] Focus chain M [auth C] Focus chain Q [auth D] Focus chain U [auth D] Focus chain V [auth E]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] SDF format, chain R [auth D] SDF format, chain W [auth E] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] MOL2 format, chain R [auth D] MOL2 format, chain W [auth E]	F [auth A], J [auth B], N [auth C], R [auth D], W [auth E]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain W [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Focus chain R [auth D] Focus chain W [auth E]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] SDF format, chain S [auth D] SDF format, chain X [auth E] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] MOL2 format, chain S [auth D] MOL2 format, chain X [auth E]	G [auth A], K [auth B], O [auth C], S [auth D], X [auth E]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain X [auth E] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Focus chain S [auth D] Focus chain X [auth E]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain Y [auth E] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain Y [auth E]	H [auth A], L [auth B], P [auth C], T [auth D], Y [auth E]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain Y [auth E] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain Y [auth E]