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- EMDB-54871: F-actin in complex with USP54 M1 actin binding motif -

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Basic information

Entry
Database: EMDB / ID: EMD-54871
TitleF-actin in complex with USP54 M1 actin binding motif
Map data
Sample
  • Complex: F-actin-USP54_M1
    • Protein or peptide: Actin binding motif
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsActin / STRUCTURAL PROTEIN
Function / homology
Function and homology information


striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / actin cytoskeleton / 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 speciesHomo sapiens (human) / Gallus gallus (chicken)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsYuan B / Paraschiakos T / Windhorst S / Marlovits TC
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Cell Biol / Year: 2026
Title: Evolutionarily conserved short linear motifs drive actin filament binding.
Authors: Themistoklis Paraschiakos / Biao Yuan / Michael Hecht-Bucher / Kostiantyn Sopelniak / Pasquale Cervero / Lisa Simon / Ksenija Zonjic / Dominic Eggers / Franziska Selle / Jing Li / Ali ...Authors: Themistoklis Paraschiakos / Biao Yuan / Michael Hecht-Bucher / Kostiantyn Sopelniak / Pasquale Cervero / Lisa Simon / Ksenija Zonjic / Dominic Eggers / Franziska Selle / Jing Li / Ali Biabani / Stefan Linder / Thomas C Marlovits / Sabine Windhorst /
Abstract: Regulation of the actin cytoskeleton by actin-binding proteins is essential for cellular homeostasis, and the mode of actin binding determines the activity of actin-binding proteins. Here we identify ...Regulation of the actin cytoskeleton by actin-binding proteins is essential for cellular homeostasis, and the mode of actin binding determines the activity of actin-binding proteins. Here we identify a 'short linear actin filament-binding motif' (SFM) based on the cryo-electron microscopy structure of the ITPKA-actin filament complex. Using the computational pipeline SLiMFold, we discovered 103 human proteins containing SFMs with diverse cellular roles. Phylogenetic analysis suggests that SFMs arose de novo and are conserved across eukaryotes, exhibiting actin filament-binding affinities of 2-12 µM. Critical residues mediating binding and modulating affinity were defined, and the cryo-electron microscopy structures of two SFM-actin filament complexes revealed that SFM binding decreases actin-filament stiffness. These findings indicate that SFMs regulate actin-filament conformation and serve as anchoring modules that connect actin dynamics to a broad variety of cellular functions, providing a framework for understanding the actin-associated roles of numerous proteins.
History
DepositionAug 22, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54871.png

Downloads & links

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Map

FileDownload / File: emd_54871.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.91 Å/pix.
x 256 pix.
= 232.96 Å		0.91 Å/pix.
x 256 pix.
= 232.96 Å		0.91 Å/pix.
x 256 pix.
= 232.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.91 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.30268943 - 0.6557472
Average (Standard dev.)0.0012539824 (±0.030460518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 232.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54871_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54871_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F-actin-USP54_M1

EntireName: F-actin-USP54_M1
Components
  • Complex: F-actin-USP54_M1
    • Protein or peptide: Actin binding motif
    • Protein or peptide: Actin, alpha skeletal muscle
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: F-actin-USP54_M1

SupramoleculeName: F-actin-USP54_M1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Actin binding motif

MacromoleculeName: Actin binding motif / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.529469 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MIPSTKGSVR SLIEQFERIQ GVSAGDPPVA TSVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG I DFKEDGNI ...String:
MIPSTKGSVR SLIEQFERIQ GVSAGDPPVA TSVSKGEELF TGVVPILVEL DGDVNGHKFS VSGEGEGDAT YGKLTLKFIC TTGKLPVPW PTLVTTLTYG VQCFSRYPDH MKQHDFFKSA MPEGYVQERT IFFKDDGNYK TRAEVKFEGD TLVNRIELKG I DFKEDGNI LGHKLEYNYN SHNVYIMADK QKNGIKVNFK IRHNIEDGSV QLADHYQQNT PIGDGPVLLP DNHYLSTQSA LS KDPNEKR DHMVLLEFVT AAGITLGMDE LYKADENLYF QGGGSGGSSK HHHHSGHHHT GHHH

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Gallus gallus (chicken)
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 #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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / 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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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm

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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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 111239
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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