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- EMDB-11787: Cryo-EM structure of F-actin stabilized by cis-optoJASP-8 -

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Basic information

Entry
Database: EMDB / ID: EMD-11787
TitleCryo-EM structure of F-actin stabilized by cis-optoJASP-8
Map dataSharpened map of the full filament filtered to local resolution. Bfactor optimised for optoJASP.
Sample
  • Complex: Filamentous alpha actin stabilized by cis-optoJASP-8 in complex with ADP-Pi
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
  • Ligand: ~{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
KeywordsCytoskeleton / jasplakinolide / azobenzene photoswitch / stabilized-actin filament / STRUCTURAL PROTEIN
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / 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
Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodhelical reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPospich S / Raunser S
Funding support Germany, 2 items
OrganizationGrant numberCountry
Max Planck Society Germany
European Union (EU)615984 Germany
CitationJournal: 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
DepositionSep 24, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0082
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0082
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ahn
  • Surface level: 0.0082
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ahn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11787.png

Downloads & links

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Map

FileDownload / File: emd_11787.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of the full filament filtered to local resolution. Bfactor optimised for optoJASP.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å		1.05 Å/pix.
x 256 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0082 / Movie #1: 0.0082
Minimum - Maximum-0.02462169 - 0.053917035
Average (Standard dev.)0.00018386025 (±0.0016726394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z268.800268.800268.800
α/β/γ90.00090.00090.000
start NX/NY/NZ1081340
NX/NY/NZ13584349
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0250.0540.000

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Supplemental data

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Mask #1

Fileemd_11787_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of the central 120A of the...

Fileemd_11787_additional_1.map
AnnotationSharpened map of the central 120A of the filament filtered to nominal resolution. Automatic Bfactor.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map of the central 120A of the...

Fileemd_11787_additional_2.map
AnnotationSharpened map of the central 120A of the filament filtered to nominal resolution. Bfactor optimised for optoJASP.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the full filament.

Fileemd_11787_half_map_1.map
AnnotationHalf map of the full filament.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map of the full filament.

Fileemd_11787_half_map_2.map
AnnotationHalf map of the full filament.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Filamentous alpha actin stabilized by cis-optoJASP-8 in complex w...

EntireName: Filamentous alpha actin stabilized by cis-optoJASP-8 in complex with ADP-Pi
Components
  • Complex: Filamentous alpha actin stabilized by cis-optoJASP-8 in complex with ADP-Pi
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
  • Ligand: ~{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

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Supramolecule #1: Filamentous alpha actin stabilized by cis-optoJASP-8 in complex w...

SupramoleculeName: 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

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 42.109973 KDa
SequenceString: 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

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Macromolecule #5: ~{N}-[4-[(4~{R},7~{R},10~{S},13~{S},15~{E},19~{S})-4-(4-hydroxyph...

MacromoleculeName: ~{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 weightTheoretical: 1.073239 KDa
Chemical component information

ChemComp-RLZ:
~{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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
5.0 mMC4H11NO3TRIS
2.0 mMNaN3Sodium azide
1.0 mMC4H10O2S2DTT
100.0 mMKClPotassium chloride
2.0 mMMgCl2Magnesium chloride
0.4 % (v/v)C2H6OSDMSO
0.02 % (v/w)C58H114O26Tween 20

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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen 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..
DetailsRise 27.5 A, Twist -166.8 degrees

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.5 Å
Applied symmetry - Helical parameters - Δ&Phi: 166.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE (ver. 1.2) / Software - details: sp_meridien_alpha.py / Number images used: 676237
Segment selectionNumber selected: 806158
Startup modelType of model: INSILICO MODEL
In silico model: Initial model was generated from PDB 5ONV and filtered to 25 A using SPARX/EMAN2.
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPHIRE (ver. 1.2) / Software - details: sp_meridien_alpha.py
Details: No helical symmetry was applied. See original publication for details.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6fhl


Chain - Chain ID: C / Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsAn initial model of cis-opto-ASP-8 was generated using elBow within Phenix inputting the SMILES string.
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7ahn:
Cryo-EM structure of F-actin stabilized by cis-optoJASP-8

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