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- PDB-9qgk: F-actin decorated by ITPKA -

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Basic information

Entry
Database: PDB / ID: 9qgk
TitleF-actin decorated by ITPKA
Components
  • Actin, alpha skeletal muscle
  • Inositol-trisphosphate 3-kinase A
  • Phalloidin
KeywordsCYTOSOLIC PROTEIN / actin
Function / homology
Function and homology information


inositol-trisphosphate 3-kinase / inositol-1,4,5-trisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / modification of postsynaptic actin cytoskeleton / postsynaptic actin cytoskeleton / calcium/calmodulin-dependent protein kinase activity / phosphatidylinositol phosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / striated muscle thin filament ...inositol-trisphosphate 3-kinase / inositol-1,4,5-trisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / modification of postsynaptic actin cytoskeleton / postsynaptic actin cytoskeleton / calcium/calmodulin-dependent protein kinase activity / phosphatidylinositol phosphate biosynthetic process / Synthesis of IP3 and IP4 in the cytosol / striated muscle thin filament / skeletal muscle thin filament assembly / skeletal muscle fiber development / stress fiber / cellular response to calcium ion / actin filament / response to calcium ion / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / small GTPase binding / structural constituent of cytoskeleton / actin cytoskeleton / dendritic spine / cytoskeleton / calmodulin binding / hydrolase activity / glutamatergic synapse / signal transduction / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family ...Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / 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
ADENOSINE-5'-DIPHOSPHATE / Inositol-trisphosphate 3-kinase A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus (bird)
Amanita phalloides (death cap)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsYuan, B. / Paraschiakos, T. / Windhorst, S. / Marlovits, T.C.
Funding support1items
OrganizationGrant numberCountry
German Research Foundation (DFG)
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
DepositionMar 13, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Part number: 1 / Data content type: FSC / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol-trisphosphate 3-kinase A
B: Inositol-trisphosphate 3-kinase A
C: Inositol-trisphosphate 3-kinase A
D: Inositol-trisphosphate 3-kinase A
E: Inositol-trisphosphate 3-kinase A
F: Actin, alpha skeletal muscle
G: Actin, alpha skeletal muscle
H: Actin, alpha skeletal muscle
I: Actin, alpha skeletal muscle
J: Actin, alpha skeletal muscle
X: Phalloidin
Y: Phalloidin
Z: Phalloidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,65323
Polymers468,39613
Non-polymers2,25810
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Inositol-trisphosphate 3-kinase A


Mass: 51083.820 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITPKA
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P23677
#2: Protein
Actin, alpha skeletal muscle / Alpha-actin-1


Mass: 42109.973 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus (bird) / Gene: ACTA1, ACTA / Production host: Gallus (bird)
References: UniProt: P68139, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#3: Protein/peptide Phalloidin


Mass: 808.899 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amanita phalloides (death cap) / Production host: Amanita phalloides (death cap)
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: F-actin decorated by ITPKA / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -166.86 ° / Axial rise/subunit: 27.58 Å / Axial symmetry: C1
3D reconstructionResolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 65917 / Symmetry type: HELICAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 44.11 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002415966
ELECTRON MICROSCOPYf_angle_d0.522821660
ELECTRON MICROSCOPYf_chiral_restr0.04132420
ELECTRON MICROSCOPYf_plane_restr0.00322761
ELECTRON MICROSCOPYf_dihedral_angle_d8.49812236

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