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- EMDB-53133: F-actin decorated by ITPKA -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-53133
TitleF-actin decorated by ITPKA
Map data
Sample
  • Complex: F-actin decorated by ITPKA
    • Protein or peptide: Inositol-trisphosphate 3-kinase A
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Phalloidin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsactin / CYTOSOLIC PROTEIN
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 / Regulation of CDH1 Function / inositol metabolic process / modification of postsynaptic actin cytoskeleton / Striated Muscle Contraction / positive regulation of dendritic spine morphogenesis / postsynaptic actin cytoskeleton ...inositol-trisphosphate 3-kinase / inositol-1,4,5-trisphosphate 3-kinase activity / inositol hexakisphosphate kinase activity / inositol phosphate biosynthetic process / Regulation of CDH1 Function / inositol metabolic process / modification of postsynaptic actin cytoskeleton / Striated Muscle Contraction / positive regulation of dendritic spine morphogenesis / postsynaptic actin cytoskeleton / calcium/calmodulin-dependent protein kinase activity / dendritic spine maintenance / 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 / regulation of synaptic plasticity / response to calcium ion / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / small GTPase binding / actin cytoskeleton / actin cytoskeleton organization / dendritic spine / cytoskeleton / calmodulin binding / hydrolase activity / glutamatergic synapse / signal transduction / ATP binding / nucleus / cytoplasm / cytosol
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
Inositol-trisphosphate 3-kinase A / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human) / Gallus (bird) / Amanita phalloides (death cap)
Methodhelical reconstruction / cryo EM / Resolution: 2.97 Å
AuthorsYuan B / Paraschiakos T / Windhorst S / Marlovits TC
Funding support1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)
CitationJournal: To Be Published
Title: F-actin decorated by ITPKA
Authors: Yuan B / Paraschiakos T / Windhorst S / Marlovits TC
History
DepositionMar 13, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53133.png

Downloads & links

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Map

FileDownload / File: emd_53133.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å		0.83 Å/pix.
x 360 pix.
= 297.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00166
Minimum - Maximum-0.011432645 - 0.036368273
Average (Standard dev.)0.00009821905 (±0.0010375605)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 297.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_53133_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53133_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : F-actin decorated by ITPKA

EntireName: F-actin decorated by ITPKA
Components
  • Complex: F-actin decorated by ITPKA
    • Protein or peptide: Inositol-trisphosphate 3-kinase A
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Phalloidin
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: F-actin decorated by ITPKA

SupramoleculeName: F-actin decorated by ITPKA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Inositol-trisphosphate 3-kinase A

MacromoleculeName: Inositol-trisphosphate 3-kinase A / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.08382 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MTLPGGPTGM ARPGGARPCS PGLERAPRRS VGELRLLFEA RCAAVAAAAA AGEPRARGAK RRGGQVPNGL PRAPPAPVIP QLTVTAEEP DVPPTSPGPP ERERDCLPAA GSSHLQQPRR LSTSSVSSTG SSSLLEDSED DLLSDSESRS RGNVQLEAGE D VGQKNHWQ ...String:
MTLPGGPTGM ARPGGARPCS PGLERAPRRS VGELRLLFEA RCAAVAAAAA AGEPRARGAK RRGGQVPNGL PRAPPAPVIP QLTVTAEEP DVPPTSPGPP ERERDCLPAA GSSHLQQPRR LSTSSVSSTG SSSLLEDSED DLLSDSESRS RGNVQLEAGE D VGQKNHWQ KIRTMVNLPV ISPFKKRYAW VQLAGHTGSF KAAGTSGLIL KRCSEPERYC LARLMADALR GCVPAFHGVV ER DGESYLQ LQDLLDGFDG PCVLDCKMGV RTYLEEELTK ARERPKLRKD MYKKMLAVDP EAPTEEEHAQ RAVTKPRYMQ WRE GISSST TLGFRIEGIK KADGSCSTDF KTTRSREQVL RVFEEFVQGD EEVLRRYLNR LQQIRDTLEV SEFFRRHEVI GSSL LFVHD HCHRAGVWLI DFGKTTPLPD GQILDHRRPW EEGNREDGYL LGLDNLIGIL ASLAER

UniProtKB: Inositol-trisphosphate 3-kinase A

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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 (bird)
Molecular weightTheoretical: 42.109973 KDa
Recombinant expressionOrganism: Gallus (bird)
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: Phalloidin

MacromoleculeName: Phalloidin / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Amanita phalloides (death cap)
Molecular weightTheoretical: 808.899 Da
Recombinant expressionOrganism: Amanita phalloides (death cap)
SequenceString:
(HYP)AW(G5G)A(ALO)C

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / 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: 8
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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: 3.0 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 27.58 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.86 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65917
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7bt7

Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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