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- EMDB-78879: Two AIP1 bound to the Barbed End of cofilin actin -

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Basic information

Entry
Database: EMDB / ID: EMD-78879
TitleTwo AIP1 bound to the Barbed End of cofilin actin
Map dataConsensus map for Two AIP1 bound to the Barbed End of cofilin actin.
Sample
  • Complex: Two AIP1 bound to the Barbed End of cofilin actin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Actin-interacting protein 1
    • Protein or peptide: Cofilin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsactin / cofilin / AIP1 / STRUCTURAL PROTEIN
Function / homology
Function and homology information


muscle thin filament assembly / positive regulation of actin filament depolymerization / negative regulation of actin filament polymerization / regulation of locomotion / actin filament depolymerization / locomotion / sarcomere organization / cytoskeletal motor activator activity / cortical actin cytoskeleton / myosin heavy chain binding ...muscle thin filament assembly / positive regulation of actin filament depolymerization / negative regulation of actin filament polymerization / regulation of locomotion / actin filament depolymerization / locomotion / sarcomere organization / cytoskeletal motor activator activity / cortical actin cytoskeleton / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / sarcoplasm / myofibril / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin filament bundle assembly / actin monomer binding / skeletal muscle fiber development / actin filament polymerization / stress fiber / titin binding / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / actin filament binding / lamellipodium / actin binding / cell body / protein domain specific binding / hydrolase activity / positive regulation of gene expression / calcium ion binding / magnesium ion binding / ATP binding / identical protein binding / cytoplasm
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 / WD domain, G-beta repeat ...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 / WD domain, G-beta repeat / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Actin, alpha skeletal muscle / Actin-interacting protein 1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsStukey GJ / Dominguez R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM161161 United States
CitationJournal: To Be Published
Title: AIP1 Promotes Severing of Cofilin-Decorated Actin Filaments by Creating a Stress-Sensitive Rigid-Compliant Boundary
Authors: Stukey GJ / Geng S / Palmer NJ / Saks A / Vavylonis D / Ono S / Dominguez R
History
DepositionAug 31, 2026-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_78879.png

Downloads & links

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Map

FileDownload / File: emd_78879.map.gz / Format: CCP4 / Size: 347.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus map for Two AIP1 bound to the Barbed End of cofilin actin.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 450 pix.
= 328.5 Å		0.73 Å/pix.
x 450 pix.
= 328.5 Å		0.73 Å/pix.
x 450 pix.
= 328.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0445
Minimum - Maximum-0.0745625 - 0.24534127
Average (Standard dev.)0.0006976233 (±0.009017766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 328.5 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A for Two AIP1 bound to the Barbed End of cofilin actin.

Fileemd_78879_half_map_1.map
AnnotationHalf map A for Two AIP1 bound to the Barbed End of cofilin actin.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B for Two AIP1 bound to the Barbed End of cofilin actin.

Fileemd_78879_half_map_2.map
AnnotationHalf map B for Two AIP1 bound to the Barbed End of cofilin 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 : Two AIP1 bound to the Barbed End of cofilin actin

EntireName: Two AIP1 bound to the Barbed End of cofilin actin
Components
  • Complex: Two AIP1 bound to the Barbed End of cofilin actin
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Actin-interacting protein 1
    • Protein or peptide: Cofilin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Two AIP1 bound to the Barbed End of cofilin actin

SupramoleculeName: Two AIP1 bound to the Barbed End of cofilin actin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 42.096953 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: Actin-interacting protein 1

MacromoleculeName: Actin-interacting protein 1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 65.392883 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MSEFSQTALF PSLPRTARGT AVVLGNTPAG DKIQYCNGTS VYTVPVGSLT DTEIYTEHSH QTTVAKTSPS GYYCASGDVH GNVRIWDTT QTTHILKTTI PVFSGPVKDI SWDSESKRIA AVGEGRERFG HVFLFDTGTS NGNLTGQARA MNSVDFKPSR P FRIISGSD ...String:
MSEFSQTALF PSLPRTARGT AVVLGNTPAG DKIQYCNGTS VYTVPVGSLT DTEIYTEHSH QTTVAKTSPS GYYCASGDVH GNVRIWDTT QTTHILKTTI PVFSGPVKDI SWDSESKRIA AVGEGRERFG HVFLFDTGTS NGNLTGQARA MNSVDFKPSR P FRIISGSD DNTVAIFEGP PFKFKSTFGE HTKFVHSVRY NPDGSLFAST GGDGTIVLYN GVDGTKTGVF EDDSLKNVAH SG SVFGLTW SPDGTKIASA SADKTIKIWN VATLKVEKTI PVGTRIEDQQ LGIIWTKQAL VSISANGFIN FVNPELGSID QVR YGHNKA ITALSSSADG KTLFSADAEG HINSWDISTG ISNRVFPDVH ATMITGIKTT SKGDLFTVSW DDHLKVVPAG GSGV DSSKA VANKLSSQPL GLAVSADGDI AVAACYKHIA IYSHGKLTEV PISYNSSCVA LSNDKQFVAV GGQDSKVHVY KLSGA SVSE VKTIVHPAEI TSVAFSNNGA FLVATDQSRK VIPYSVANNF ELAHTNSWTF HTAKVACVSW SPDNVRLATG SLDNSV IVW NMNKPSDHPI IIKGAHAMSS VNSVIWLNET TIVSAGQDSN IKFWNVPF

UniProtKB: Actin-interacting protein 1

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Macromolecule #3: Cofilin

MacromoleculeName: Cofilin / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Molecular weightTheoretical: 17.070465 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MASGVKVDPS CKNAYDLLHN KHQHSYIIFK IDKNDTAIVV EKVGEKNAPY AEFVEEMKKL VEDGKECRYA AVDVEVTVQR QGAEGTSTL NKVIFVQYCP DNAPVRRRML YASSVRALKA SLGLESLFQV QASEMSDLDE KSVKSDLMSN QRI

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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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Macromolecule #5: MAGNESIUM ION

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

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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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 51.71 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 42984
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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