[English] 日本語
Yorodumi
- EMDB-72706: Capping protein bound to the barbed end of cofilactin, co-bound w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72706
TitleCapping protein bound to the barbed end of cofilactin, co-bound with cofilin on the B-1 actin, consensus map
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
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 / Advanced glycosylation endproduct receptor signaling / actin filament bundle assembly / 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: To Be Published
Title: Mechanisms of Actin Filament Depolymerization by Cyclase Associated Protein-1 and Cofilin-2
Authors: Palmer NJ / Boczkowska M / Rebowski G / Dominguez R
History
DepositionSep 14, 2025-
Header (metadata) releaseMar 11, 2026-
Map releaseMar 11, 2026-
UpdateMar 11, 2026-
Current statusMar 11, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72706.png

Downloads & links

-
Map

FileDownload / File: emd_72706.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 416 pix.
= 446.784 Å		1.07 Å/pix.
x 416 pix.
= 446.784 Å		1.07 Å/pix.
x 416 pix.
= 446.784 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0569
Minimum - Maximum-0.095900565 - 0.3560972
Average (Standard dev.)0.00019228677 (±0.008259043)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 446.784 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_72706_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_72706_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_72706_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
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: all

-
Supramolecule #2: Actin, alpha skeletal muscle

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

-
Supramolecule #3: Cofilin-2

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

-
Supramolecule #4: Capping Protein

SupramoleculeName: Capping Protein / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
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

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

MacromoleculeName: F-actin-capping protein subunit alpha-1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLDP RNKISFKFDH LRKEASDPQP EEADGGLKSW RESCDSALRA YVKDHYSNGF CTVYAKTIDG QQTIIACIES HQFQPKNFWN ...String:
MADFDDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY EDQVLITEHG DLGNSRFLDP RNKISFKFDH LRKEASDPQP EEADGGLKSW RESCDSALRA YVKDHYSNGF CTVYAKTIDG QQTIIACIES HQFQPKNFWN GRWRSEWKFT ITPPTAQVVG VLKIQVHYYE DGNVQLVSHK DVQDSLTVSN EAQTAKEFIK IIENAENEYQ TAISENYQTM SDTTFKALRR QLPVTRTKID WNKILSYKIG KEMQNA

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

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

MacromoleculeName: F-actin-capping protein subunit beta / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGD SYRSPWSNKY DPPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV Y LWDLDHGF AGVILIKKAG DGSKKIKGCW DSIHVVEVQE KSSGRTAHYK ...String:
MSDQQLDCAL DLMRRLPPQQ IEKNLSDLID LVPSLCEDLL SSVDQPLKIA RDKVVGKDYL LCDYNRDGD SYRSPWSNKY DPPLEDGAMP SARLRKLEVE ANNAFDQYRD LYFEGGVSSV Y LWDLDHGF AGVILIKKAG DGSKKIKGCW DSIHVVEVQE KSSGRTAHYK LTSTVMLWLQ TN KSGSGTM NLGGSLTRQM EKDETVSDCS PHIANIGRLV EDMENKIRST LNEIYFGKTK DIV NGLRSV QTFADKSKQE ALKNDLVEAL KRKQQC

UniProtKB: F-actin-capping protein subunit beta

-
Macromolecule #4: Cofilin-2

MacromoleculeName: Cofilin-2 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

-
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

-
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

+
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)
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more