+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11787 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of F-actin stabilized by cis-optoJASP-8 | |||||||||
Map data | Sharpened map of the full filament filtered to local resolution. Bfactor optimised for optoJASP. | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly ...cytoskeletal motor activator activity / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / hydrolase activity / protein domain specific binding / calcium ion binding / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Rabbit (rabbit) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Pospich S / Raunser S | |||||||||
Funding support | Germany, 2 items
| |||||||||
Citation | Journal: Angew Chem Int Ed Engl / Year: 2021 Title: Cryo-EM Resolves Molecular Recognition Of An Optojasp Photoswitch Bound To Actin Filaments In Both Switch States. Authors: Sabrina Pospich / Florian Küllmer / Veselin Nasufović / Johanna Funk / Alexander Belyy / Peter Bieling / Hans-Dieter Arndt / Stefan Raunser / 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 ...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. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_11787.map.gz | 2.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-11787-v30.xml emd-11787.xml | 25.9 KB 25.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11787_fsc.xml | 9.4 KB | Display | FSC data file |
Images | emd_11787.png | 114.2 KB | ||
Masks | emd_11787_msk_1.map | 64 MB | Mask map | |
Others | emd_11787_additional_1.map.gz emd_11787_additional_2.map.gz emd_11787_half_map_1.map.gz emd_11787_half_map_2.map.gz | 4.5 MB 4.5 MB 30.8 MB 30.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11787 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11787 | HTTPS FTP |
-Related structure data
Related structure data | 7ahnMC 7ahqC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_11787.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map of the full filament filtered to local resolution. Bfactor optimised for optoJASP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_11787_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Sharpened map of the central 120A of the...
File | emd_11787_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map of the central 120A of the filament filtered to nominal resolution. Automatic Bfactor. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Sharpened map of the central 120A of the...
File | emd_11787_additional_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Sharpened map of the central 120A of the filament filtered to nominal resolution. Bfactor optimised for optoJASP. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map of the full filament.
File | emd_11787_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map of the full filament. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: Half map of the full filament.
File | emd_11787_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Half map of the full filament. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Filamentous alpha actin stabilized by cis-optoJASP-8 in complex w...
Entire | Name: Filamentous alpha actin stabilized by cis-optoJASP-8 in complex with ADP-Pi |
---|---|
Components |
|
-Supramolecule #1: Filamentous alpha actin stabilized by cis-optoJASP-8 in complex w...
Supramolecule | Name: Filamentous alpha actin stabilized by cis-optoJASP-8 in complex with ADP-Pi type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Rabbit (rabbit) |
Molecular weight | Theoretical: 42.109973 KDa |
Sequence | String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: PO4 |
---|---|
Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ChemComp-PO4: |
-Macromolecule #5: ~{N}-[4-[(4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-4-(4-hydroxyph...
Macromolecule | Name: ~{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- ...Name: ~{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 type: ligand / ID: 5 / Number of copies: 5 / Formula: RLZ |
---|---|
Molecular weight | Theoretical: 1.073239 KDa |
Chemical component information | ChemComp-RLZ: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 Component:
Details: 5 mM Tris pH 7.5, 2 mM NaN3, 1 mM DTT, 100 mM KCl and 2 mM MgCl2, 0.4 %(v/v) DMSO, 0.02 %(v/w) Tween 20 | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK III Details: 1.5 mul sample, automatic blotting for 7-7.5s, blot force -25, drain time 1s.. | ||||||||||||||||||||||||
Details | Rise 27.5 A, Twist -166.8 degrees |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 4771 / Average exposure time: 15.0 sec. / Average electron dose: 86.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |