[English] 日本語
Yorodumi
- EMDB-13343: Structure of capping protein bound to the barbed end of a cytopla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13343
TitleStructure of capping protein bound to the barbed end of a cytoplasmic actin filament
Map dataLocally filtered map with global B-factor
Sample
  • Complex: Complex between capping protein and the barbed end of cytoplasmic actin filaments
    • Protein or peptide: Isoform 2 of F-actin-capping protein subunit beta
    • Protein or peptide: F-actin-capping protein subunit alpha-1
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Phalloidin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION
Function / homology
Function and homology information


cytoskeletal calyx / regulation of protein kinase C signaling / Cell-extracellular matrix interactions / Formation of the dystrophin-glycoprotein complex (DGC) / Adherens junctions interactions / Advanced glycosylation endproduct receptor signaling / B-WICH complex positively regulates rRNA expression / RHOF GTPase cycle / Gap junction degradation / Formation of annular gap junctions ...cytoskeletal calyx / regulation of protein kinase C signaling / Cell-extracellular matrix interactions / Formation of the dystrophin-glycoprotein complex (DGC) / Adherens junctions interactions / Advanced glycosylation endproduct receptor signaling / B-WICH complex positively regulates rRNA expression / RHOF GTPase cycle / Gap junction degradation / Formation of annular gap junctions / RHOD GTPase cycle / MAP2K and MAPK activation / RHOF GTPase cycle / COPI-independent Golgi-to-ER retrograde traffic / EPHB-mediated forward signaling / Regulation of actin dynamics for phagocytic cup formation / RHO GTPases Activate WASPs and WAVEs / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / F-actin capping protein complex / WASH complex / COPI-mediated anterograde transport / sperm head-tail coupling apparatus / DNA Damage Recognition in GG-NER / UCH proteinases / sperm head / VEGFA-VEGFR2 Pathway / Factors involved in megakaryocyte development and platelet production / structural constituent of postsynaptic actin cytoskeleton / Clathrin-mediated endocytosis / barbed-end actin filament capping / dense body / cell projection organization / cell junction assembly / MHC class II antigen presentation / actin polymerization or depolymerization / muscle cell development / regulation of cell morphogenesis / lamellipodium assembly / negative regulation of microtubule polymerization / NuA4 histone acetyltransferase complex / cortical cytoskeleton / beta-tubulin binding / brush border / asymmetric synapse / intercalated disc / cytoskeleton organization / axonogenesis / hippocampal mossy fiber to CA3 synapse / actin filament / cell motility / Schaffer collateral - CA1 synapse / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / Z disc / neuron projection development / cell-cell junction / lamellipodium / actin cytoskeleton / actin binding / cytoskeleton / hydrolase activity / postsynaptic density / axon / focal adhesion / synapse / protein kinase binding / protein-containing complex / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm
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 alpha-1 / F-actin-capping protein subunit beta / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesMus musculus (house mouse) / Bovine (domestic cattle) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsFunk J / Merino F / Schacks M / Rottner K / Raunser S / Bieling P
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2021
Title: A barbed end interference mechanism reveals how capping protein promotes nucleation in branched actin networks.
Authors: Johanna Funk / Felipe Merino / Matthias Schaks / Klemens Rottner / Stefan Raunser / Peter Bieling /
Abstract: Heterodimeric capping protein (CP/CapZ) is an essential factor for the assembly of branched actin networks, which push against cellular membranes to drive a large variety of cellular processes. Aside ...Heterodimeric capping protein (CP/CapZ) is an essential factor for the assembly of branched actin networks, which push against cellular membranes to drive a large variety of cellular processes. Aside from terminating filament growth, CP potentiates the nucleation of actin filaments by the Arp2/3 complex in branched actin networks through an unclear mechanism. Here, we combine structural biology with in vitro reconstitution to demonstrate that CP not only terminates filament elongation, but indirectly stimulates the activity of Arp2/3 activating nucleation promoting factors (NPFs) by preventing their association to filament barbed ends. Key to this function is one of CP's C-terminal "tentacle" extensions, which sterically masks the main interaction site of the terminal actin protomer. Deletion of the β tentacle only modestly impairs capping. However, in the context of a growing branched actin network, its removal potently inhibits nucleation promoting factors by tethering them to capped filament ends. End tethering of NPFs prevents their loading with actin monomers required for activation of the Arp2/3 complex and thus strongly inhibits branched network assembly both in cells and reconstituted motility assays. Our results mechanistically explain how CP couples two opposed processes-capping and nucleation-in branched actin network assembly.
History
DepositionAug 9, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7pdz
  • Surface level: 0.045
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pdz
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13343.png

Downloads & links

-
Map

FileDownload / File: emd_13343.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLocally filtered map with global B-factor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 384 pix.
= 464.64 Å		1.21 Å/pix.
x 384 pix.
= 464.64 Å		1.21 Å/pix.
x 384 pix.
= 464.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum-0.08255227 - 0.21015494
Average (Standard dev.)-0.00014572637 (±0.0043614074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 464.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.211.211.21
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z464.640464.640464.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ640640640
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0830.210-0.000

-
Supplemental data

-
Mask #1

Fileemd_13343_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Locally filtered map using deepEMhancer's high resolution model

Fileemd_13343_additional_1.map
AnnotationLocally filtered map using deepEMhancer's high resolution model
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Map filtered globally to a resolution of 3.9 A

Fileemd_13343_additional_2.map
AnnotationMap filtered globally to a resolution of 3.9 A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_13343_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_13343_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex between capping protein and the barbed end of cytoplasmic...

EntireName: Complex between capping protein and the barbed end of cytoplasmic actin filaments
Components
  • Complex: Complex between capping protein and the barbed end of cytoplasmic actin filaments
    • Protein or peptide: Isoform 2 of F-actin-capping protein subunit beta
    • Protein or peptide: F-actin-capping protein subunit alpha-1
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Phalloidin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE ION

-
Supramolecule #1: Complex between capping protein and the barbed end of cytoplasmic...

SupramoleculeName: Complex between capping protein and the barbed end of cytoplasmic actin filaments
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

-
Macromolecule #1: Isoform 2 of F-actin-capping protein subunit beta

MacromoleculeName: Isoform 2 of F-actin-capping protein subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
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

-
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: Mus musculus (house mouse)
Molecular weightTheoretical: 32.980703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MADFEDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY DDQVLITEHG DLGNSRFLD PRNQISFKFD HLRKEASDPQ PEDVDGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF ...String:
MADFEDRVSD EEKVRIAAKF ITHAPPGEFN EVFNDVRLLL NNDNLLREGA AHAFAQYNMD QFTPVKIEGY DDQVLITEHG DLGNSRFLD PRNQISFKFD HLRKEASDPQ PEDVDGGLKS WRESCDSALR AYVKDHYSNG FCTVYAKTID GQQTIIACIE S HQFQPKNF WNGRWRSEWK FTITPPSAQV VGVLKIQVHY YEDGNVQLVS HKDVQDSVTV SNEVQTTKEF IKIIESAENE YQ TAISENY QTMSDTTFKA LRRQLPVTRT KIDWNKILSY KIGKEMQNA

-
Macromolecule #3: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 3 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bovine (domestic cattle)
Molecular weightTheoretical: 41.79568 KDa
SequenceString: MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG ...String:
MDDDIAALVV DNGSGMCKAG FAGDDAPRAV FPSIVGRPRH QGVMVGMGQK DSYVGDEAQS KRGILTLKYP IE(HIC)GIV TNW DDMEKIWHHT FYNELRVAPE EHPVLLTEAP LNPKANREKM TQIMFETFNT PAMYVAIQAV LSLYASGRTT GIVMDSG DG VTHTVPIYEG YALPHAILRL DLAGRDLTDY LMKILTERGY SFTTTAEREI VRDIKEKLCY VALDFEQEMA TAASSSSL E KSYELPDGQV ITIGNERFRC PEALFQPSFL GMESCGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

-
Macromolecule #4: Phalloidin

MacromoleculeName: Phalloidin / type: protein_or_peptide / ID: 4 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 808.899 Da
SequenceString:
(HYP)AW(EEP)A(DTH)C

-
Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

-
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

-
Macromolecule #7: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7
Component:
ConcentrationFormulaName
50.0 mMKClPotassium chloride
10.0 mMImidazole
1.5 mMMgCl2Magnesium chloride
1.0 mMEGTA

Details: KMEI buffer
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: Mild discharging with 5 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 2 / Number real images: 4204 / Average exposure time: 3.0 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 570724
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.13)
Startup modelType of model: OTHER
Details: Artificially built actin filament. Generated from 6FHL
Final reconstructionNumber classes used: 1 / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE (ver. 1.3) / Number images used: 60206
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE (ver. 1.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE (ver. 1.3)
Final 3D classificationNumber classes: 3 / Software - Name: SPHIRE (ver. 1.3)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

5adx

RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 40
Output model

PDB-7pdz:
Structure of capping protein bound to the barbed end of a cytoplasmic actin filament

+
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