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- EMDB-72707: CP at the barbed end with one cofilin on second-to-last subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-72707
TitleCP at the barbed end with one cofilin on second-to-last subunit
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: Cofilin-2
      • Protein or peptide: Cofilin-2
    • 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
KeywordsCytoskeleton / Actin / Filament / Helical / PROTEIN FIBRIL
Function / homology
Function and homology information


actin filament fragmentation / F-actin capping protein complex / WASH complex / positive regulation of actin filament depolymerization / actin filament severing / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament depolymerization / RHOD GTPase cycle ...actin filament fragmentation / F-actin capping protein complex / WASH complex / positive regulation of actin filament depolymerization / actin filament severing / cell junction assembly / barbed-end actin filament capping / actin polymerization or depolymerization / actin filament depolymerization / RHOD GTPase cycle / regulation of cell morphogenesis / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic / lamellipodium assembly / I band / Sensory processing of sound by inner hair cells of the cochlea / cytoskeletal motor activator activity / sarcomere organization / muscle cell cellular homeostasis / 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 / skeletal muscle tissue development / 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 / Z disc / nuclear matrix / 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 / ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / ADF-H/Gelsolin-like domain superfamily / 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 / Cofilin-2
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 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
DepositionSep 14, 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_72707.png

Downloads & links

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Map

FileDownload / File: emd_72707.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.54 Å/pix.
x 640 pix.
= 345.6 Å		0.54 Å/pix.
x 640 pix.
= 345.6 Å		0.54 Å/pix.
x 640 pix.
= 345.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.54 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.078
Minimum - Maximum-0.07525485 - 0.36163214
Average (Standard dev.)0.0034184796 (±0.011459471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

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Supplemental data

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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: Cofilin-2
      • Protein or peptide: Cofilin-2
    • 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

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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-#4

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Supramolecule #2: Actin, alpha skeletal muscle

SupramoleculeName: Actin, alpha skeletal muscle / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1

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Supramolecule #3: Cofilin-2

SupramoleculeName: Cofilin-2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #4: Capping Protein

SupramoleculeName: Capping Protein / type: complex / ID: 4 / 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: 41.978773 KDa
SequenceString: CDEDETTALV CDNGSGLVKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIE(HIC)GI ITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDS GD GVTHNVPIYE ...String:
CDEDETTALV CDNGSGLVKA GFAGDDAPRA VFPSIVGRPR HQGVMVGMGQ KDSYVGDEAQ SKRGILTLKY PIE(HIC)GI ITN WDDMEKIWHH TFYNELRVAP EEHPTLLTEA PLNPKANREK MTQIMFETFN VPAMYVAIQA VLSLYASGRT TGIVLDS GD GVTHNVPIYE GYALPHAIMR LDLAGRDLTD YLMKILTERG YSFVTTAERE IVRDIKEKLC YVALDFENEM ATAASSSS L EKSYELPDGQ VITIGNERFR CPETLFQPSF IGMESAGIHE TTYNSIMKCD IDIRKDLYAN NVMSGGTTMY PGIADRMQK EITALAPSTM KIKIIAPPER KYSVWIGGSI LASLSTFQQM WITKQEYDEA GPSIVHRKCF

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: 32.964727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLD PRNKISFKFD HLRKEASDPQ PEEADGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF ...String:
MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLD PRNKISFKFD HLRKEASDPQ PEEADGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF WNGRWRSEWK FTITPPTAQV VGVLKIQVHY YEDGNVQLVS HKDVQDSLTV SNEAQTAKEF IKIIENAENE YQ TAISENY QTMSDTTFKA LRRQLPVTRT KIDWNKILSY KIGKEMQNA

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: 30.669768 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV YLWDLDHGFA GVILIKKAGD GSKKIKGCWD SIHVVEVQEK S SGRTAHYK ...String:
MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGDS YRSPWSNKYD PPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV YLWDLDHGFA GVILIKKAGD GSKKIKGCWD SIHVVEVQEK S SGRTAHYK LTSTVMLWLQ TNKSGSGTMN LGGSLTRQME KDETVSDCSP HIANIGRLVE DMENKIRSTL NEIYFGKTKD IV NGLRSVQ TFADKSKQEA LKNDLVEALK RKQQC

UniProtKB: F-actin-capping protein subunit beta

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Macromolecule #4: Cofilin-2

MacromoleculeName: Cofilin-2 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.765627 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MASGVTVNDE VIKVFNDMKV RKSSTQEEIK KRKKAVLFCL SDDKRQIIVE EAKQILVGDI GDTVEDPYTS FVKLLPLNDC RYALYDATY ETKESKKEDL VFIFWAPESA PLKSKMIYAS SKDAIKKKFT GIKHEWQVNG LDDIKDRSTL GEKLGGNVVV S LEGKPL

UniProtKB: Cofilin-2

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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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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / 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
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: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7) / Number images used: 67400
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)

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