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- EMDB-72998: Capping protein bound to the barbed end of F-actin -

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Basic information

Entry
Database: EMDB / ID: EMD-72998
TitleCapping protein bound to the barbed end of F-actin
Map data
Sample
  • Complex: Complex of the Cyclase Associated Protein-1 bound to F-actin
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Capping Protein
      • Protein or peptide: F-actin-capping protein subunit alpha-1
      • Protein or peptide: F-actin-capping protein subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsCytoskeleton / Actin / Filament / Helical / PROTEIN FIBRIL
Function / homology
Function and homology information


F-actin capping protein complex / WASH complex / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / RHOD GTPase cycle / regulation of cell morphogenesis / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic / lamellipodium assembly ...F-actin capping protein complex / WASH complex / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / RHOD GTPase cycle / regulation of cell morphogenesis / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic / lamellipodium assembly / Sensory processing of sound by inner hair cells of the cochlea / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / cortical cytoskeleton / skeletal muscle myofibril / brush border / actin filament bundle assembly / Advanced glycosylation endproduct receptor signaling / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / sperm head-tail coupling apparatus / COPI-mediated anterograde transport / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / cytoskeleton organization / MHC class II antigen presentation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / hippocampal mossy fiber to CA3 synapse / sarcomere / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Schaffer collateral - CA1 synapse / calcium-dependent protein binding / actin filament binding / lamellipodium / actin cytoskeleton / Factors involved in megakaryocyte development and platelet production / actin binding / actin cytoskeleton organization / cell body / protein-containing complex assembly / cytoskeleton / postsynaptic density / cadherin binding / protein domain specific binding / hydrolase activity / calcium ion binding / positive regulation of gene expression / magnesium ion binding / extracellular exosome / extracellular region / ATP binding / membrane / identical protein binding / cytoplasm / cytosol
Similarity search - Function
F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta ...F-actin-capping protein subunit beta / F-actin capping protein, beta subunit, conserved site / F-actin-capping protein subunit beta, N-terminal domain / F-actin capping protein, beta subunit / F-actin capping protein beta subunit signature. / F-actin capping protein, alpha subunit, conserved site / F-actin capping protein alpha subunit signature 1. / F-actin capping protein alpha subunit signature 2. / F-actin-capping protein subunit alpha / F-actin-capping protein subunit alpha/beta / F-actin-capping protein subunit alpha/beta, domain 2 / F-actin capping protein, alpha subunit, domain 1 / F-actin capping protein alpha subunit / 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
F-actin-capping protein subunit beta / F-actin-capping protein subunit alpha-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsPalmer NJ / Dominguez R
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Sci Adv / Year: 2026
Title: Mechanisms of disassembly at the actin filament pointed and barbed ends.
Authors: Nicholas J Palmer / Malgorzata Boczkowska / Grzegorz Rebowski / Roberto Dominguez /
Abstract: Actin cytoskeleton dynamics power processes from cell motility to organelle trafficking, requiring rapid polymerization and depolymerization accelerated in cells by regulatory proteins. While ...Actin cytoskeleton dynamics power processes from cell motility to organelle trafficking, requiring rapid polymerization and depolymerization accelerated in cells by regulatory proteins. While mechanisms of accelerated polymerization are relatively well studied, those of depolymerization remain poorly understood. Here, we present twelve cryo-electron microscopy structures showing how cofilin, cyclase-associated protein (CAP), and capping protein (CP) coordinate their activities to accelerate depolymerization at both filament ends. Alone, CAP produces a ~4.0 Å lateral displacement of the first pointed-end subunit, whereas cofilin reverts terminal subunits at the pointed and barbed ends to a G-actin-like conformation and undertwists the filament short-pitch helix. When functioning together, these cofilin- and CAP-induced conformational changes are amplified to accelerate pointed-end disassembly. At the barbed end, the cofilin-induced changes trigger stepwise CP dissociation and favor depolymerization. These findings support end-specific mechanisms of filament disassembly through accelerated subunit dissociation, slowed subunit addition, and barbed-end uncapping.
History
DepositionOct 1, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72998.png

Downloads & links

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Map

FileDownload / File: emd_72998.map.gz / Format: CCP4 / Size: 282 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
0.83 Å/pix.
x 419 pix.
= 346.932 Å		0.83 Å/pix.
x 420 pix.
= 347.76 Å		0.83 Å/pix.
x 420 pix.
= 347.76 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: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.05633937 - 0.25432998
Average (Standard dev.)0.00082007947 (±0.005638932)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions420420419
Spacing420420419
CellA: 347.76 Å / B: 347.76 Å / C: 346.932 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Composite map of consensus local refinements, averaged with...

Fileemd_72998_additional_1.map
AnnotationComposite map of consensus local refinements, averaged with sharpened composite map for use in model refinements
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Composite map of sharpened local refinements, averaged with...

Fileemd_72998_additional_2.map
AnnotationComposite map of sharpened local refinements, averaged with consensus composite map for use in model refinements
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the Cyclase Associated Protein-1 bound to F-actin

EntireName: Complex of the Cyclase Associated Protein-1 bound to F-actin
Components
  • Complex: Complex of the Cyclase Associated Protein-1 bound to F-actin
    • Complex: Actin, alpha skeletal muscle
      • Protein or peptide: Actin, alpha skeletal muscle
    • Complex: Capping Protein
      • Protein or peptide: F-actin-capping protein subunit alpha-1
      • Protein or peptide: F-actin-capping protein subunit beta
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Complex of the Cyclase Associated Protein-1 bound to F-actin

SupramoleculeName: Complex of the Cyclase Associated Protein-1 bound to F-actin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: Actin, alpha skeletal muscle

SupramoleculeName: Actin, alpha skeletal muscle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: Capping Protein

SupramoleculeName: Capping Protein / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

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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
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
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

UniProtKB: Actin, alpha skeletal muscle

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Macromolecule #2: F-actin-capping protein subunit alpha-1

MacromoleculeName: F-actin-capping protein subunit alpha-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.041746 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VSDEEKVRIA AKFITHAPPG EFNEVFNDVR LLLNNDNLLR EGAAHAFAQY NMDQFTPVKI EGYEDQVLIT EHGDLGNSRF LDPRNKISF KFDHLRKEAS DPQPEEADGG LKSWRESCDS ALRAYVKDHY SNGFCTVYAK TIDGQQTIIA CIESHQFQPK N FWNGRWRS ...String:
VSDEEKVRIA AKFITHAPPG EFNEVFNDVR LLLNNDNLLR EGAAHAFAQY NMDQFTPVKI EGYEDQVLIT EHGDLGNSRF LDPRNKISF KFDHLRKEAS DPQPEEADGG LKSWRESCDS ALRAYVKDHY SNGFCTVYAK TIDGQQTIIA CIESHQFQPK N FWNGRWRS EWKFTITPPT AQVVGVLKIQ VHYYEDGNVQ LVSHKDVQDS LTVSNEAQTA KEFIKIIENA ENEYQTAISE NY QTMSDTT FKALRRQLPV TRTKIDWNKI LSYKIGKEMQ N

UniProtKB: F-actin-capping protein subunit alpha-1

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Macromolecule #3: F-actin-capping protein subunit beta

MacromoleculeName: F-actin-capping protein subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.435432 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SDQQLDCALD LMRRLPPQQI EKNLSDLIDL VPSLCEDLLS SVDQPLKIAR DKVVGKDYLL CDYNRDGDSY RSPWSNKYDP PLEDGAMPS ARLRKLEVEA NNAFDQYRDL YFEGGVSSVY LWDLDHGFAG VILIKKAGDG SKKIKGCWDS IHVVEVQEKS S GRTAHYKL ...String:
SDQQLDCALD LMRRLPPQQI EKNLSDLIDL VPSLCEDLLS SVDQPLKIAR DKVVGKDYLL CDYNRDGDSY RSPWSNKYDP PLEDGAMPS ARLRKLEVEA NNAFDQYRDL YFEGGVSSVY LWDLDHGFAG VILIKKAGDG SKKIKGCWDS IHVVEVQEKS S GRTAHYKL TSTVMLWLQT NKSGSGTMNL GGSLTRQMEK DETVSDCSPH IANIGRLVED MENKIRSTLN EIYFGKTKDI VN GLRSVQT FADKSKQEAL KNDLVEALKR KQQ

UniProtKB: F-actin-capping protein subunit beta

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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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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 9 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 120 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 89000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 275590
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)

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