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- EMDB-27117: Bent ADP-Pi-F-actin -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-27117
TitleBent ADP-Pi-F-actin
Map dataMain map, bent ADP-Pi F-actin
Sample
  • Complex: Bent F-actin, ADP-Pi nucleotide state
    • Protein or peptide: Actin, alpha skeletal muscle, intermediate form
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
Function / homology
Function and homology information


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
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 speciesGallus gallus (chicken) / chicken (chicken)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsReynolds MJ / Alushin GM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM141044 United States
CitationJournal: Nature / Year: 2022
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
DepositionMay 26, 2022-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateNov 23, 2022-
Current statusNov 23, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27117.png

Downloads & links

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Map

FileDownload / File: emd_27117.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, bent ADP-Pi F-actin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.03 Å/pix.
x 87 pix.
= 89.61 Å		1.03 Å/pix.
x 100 pix.
= 103. Å		1.03 Å/pix.
x 247 pix.
= 254.41 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.09794458 - 0.20587902
Average (Standard dev.)0.008802947 (±0.020729475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin205140214
Dimensions10024787
Spacing87100247
CellA: 89.61 Å / B: 103.0 Å / C: 254.40999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27117_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2, bent ADP-Pi F-actin

Fileemd_27117_half_map_1.map
AnnotationHalf-map 2, bent ADP-Pi F-actin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1, bent ADP-Pi F-actin

Fileemd_27117_half_map_2.map
AnnotationHalf-map 1, bent ADP-Pi F-actin
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bent F-actin, ADP-Pi nucleotide state

EntireName: Bent F-actin, ADP-Pi nucleotide state
Components
  • Complex: Bent F-actin, ADP-Pi nucleotide state
    • Protein or peptide: Actin, alpha skeletal muscle, intermediate form
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION

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Supramolecule #1: Bent F-actin, ADP-Pi nucleotide state

SupramoleculeName: Bent F-actin, ADP-Pi nucleotide state / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Mechanically deformed filamentous actin in the ADP-Pi state
Source (natural)Organism: Gallus gallus (chicken)
Molecular weightTheoretical: 15.1 kDa/nm

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Macromolecule #1: Actin, alpha skeletal muscle, intermediate form

MacromoleculeName: Actin, alpha skeletal muscle, intermediate form / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: chicken (chicken)
Molecular weightTheoretical: 41.387227 KDa
SequenceString: TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP ...String:
TTALVCDNGS GLVKAGFAGD DAPRAVFPSI VGRPRHQGVM VGMGQKDSYV GDEAQSKRGI LTLKYPIE(HIC)G IITNWD DME KIWHHTFYNE LRVAPEEHPT LLTEAPLNPK ANREKMTQIM FETFNVPAMY VAIQAVLSLY ASGRTTGIVL DSGDGVT HN VPIYEGYALP HAIMRLDLAG RDLTDYLMKI LTERGYSFVT TAEREIVRDI KEKLCYVALD FENEMATAAS SSSLEKSY E LPDGQVITIG NERFRCPETL FQPSFIGMES AGIHETTYNS IMKCDIDIRK DLYANNVMSG GTTMYPGIAD RMQKEITAL APSTMKIKII APPERKYSVW IGGSILASLS TFQQMWITKQ EYDEAGPSIV HRKCF

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 7 / 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: 7 / 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: 7 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Startup modelType of model: NONE
Details: Ab initio reconstruction as implemented in cryoSPARC
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 14991
Initial angle assignmentType: OTHER
Details: In RELION star file format, rot randomly assigned, tilt prior set to 90, psi prior (with bimodal psi) determined by auto-picking.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3,1)
FSC plot (resolution estimation)

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