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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Helical ADP-F-actin | |||||||||
![]() | Final refine3d map, unsharpened, unboxed, unmasked | |||||||||
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Function / homology | ![]() Striated Muscle Contraction / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / hydrolase activity / ATP binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 2.43 Å | |||||||||
![]() | Reynolds MJ / Alushin GM | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Bending forces and nucleotide state jointly regulate F-actin structure. Authors: Matthew J Reynolds / Carla Hachicho / Ayala G Carl / Rui Gong / Gregory M Alushin / ![]() Abstract: ATP-hydrolysis-coupled actin polymerization is a fundamental mechanism of cellular force generation. In turn, force and actin filament (F-actin) nucleotide state regulate actin dynamics by tuning F- ...ATP-hydrolysis-coupled actin polymerization is a fundamental mechanism of cellular force generation. In turn, force and actin filament (F-actin) nucleotide state regulate actin dynamics by tuning F-actin's engagement of actin-binding proteins through mechanisms that are unclear. Here we show that the nucleotide state of actin modulates F-actin structural transitions evoked by bending forces. Cryo-electron microscopy structures of ADP-F-actin and ADP-P-F-actin with sufficient resolution to visualize bound solvent reveal intersubunit interfaces bridged by water molecules that could mediate filament lattice flexibility. Despite extensive ordered solvent differences in the nucleotide cleft, these structures feature nearly identical lattices and essentially indistinguishable protein backbone conformations that are unlikely to be discriminable by actin-binding proteins. We next introduce a machine-learning-enabled pipeline for reconstructing bent filaments, enabling us to visualize both continuous structural variability and side-chain-level detail. Bent F-actin structures reveal rearrangements at intersubunit interfaces characterized by substantial alterations of helical twist and deformations in individual protomers, transitions that are distinct in ADP-F-actin and ADP-P-F-actin. This suggests that phosphate rigidifies actin subunits to alter the bending structural landscape of F-actin. As bending forces evoke nucleotide-state dependent conformational transitions of sufficient magnitude to be detected by actin-binding proteins, we propose that actin nucleotide state can serve as a co-regulator of F-actin mechanical regulation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 409.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.6 KB 19.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.9 KB | Display | ![]() |
Images | ![]() | 127.2 KB | ||
Masks | ![]() | 512 MB | ![]() | |
Others | ![]() ![]() ![]() | 272.1 MB 410.8 MB 410.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8d13MC ![]() 8d14C ![]() 8d15C ![]() 8d16C ![]() 8d17C ![]() 8d18C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
EM raw data | ![]() Data #1: Unaligned multi-frame micrographs of ADP-F-actin [micrographs - multiframe] Data #2: Polished single-frame particles of bent ADP-F-actin segments [picked particles - single frame - processed] Data #3: Polished single-frame particles of straight ADP-F-actin segments, Subset 1 [picked particles - single frame - processed] Data #4: Polished single-frame particles of straight ADP-F-actin segments, Subset 2 [picked particles - single frame - processed] Data #5: Polished single-frame particles of helical ADP-F-actin segments, for high-resolution [picked particles - single frame - processed]) |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Final refine3d map, unsharpened, unboxed, unmasked | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.03 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Additional map: Mapboxed, 4x upsampled, density modified map to help model building
File | emd_27114_additional_1.map | ||||||||||||
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Annotation | Mapboxed, 4x upsampled, density modified map to help model building | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 2, helical ADP F-actin
File | emd_27114_half_map_1.map | ||||||||||||
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Annotation | Half map 2, helical ADP F-actin | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1, helical ADP F-actin
File | emd_27114_half_map_2.map | ||||||||||||
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Annotation | Half map 1, helical ADP F-actin | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Helical F-actin, ADP nucleotide state
Entire | Name: Helical F-actin, ADP nucleotide state |
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Components |
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-Supramolecule #1: Helical F-actin, ADP nucleotide state
Supramolecule | Name: Helical F-actin, ADP nucleotide state / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Helically symmetric filamentous actin in the aged ADP state |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.1 kDa/nm |
-Macromolecule #1: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
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: 3 / Formula: ADP |
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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: 3 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: water
Macromolecule | Name: water / type: ligand / ID: 4 / Number of copies: 432 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ![]() ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | helical reconstruction |
Aggregation state | filament |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |