[English] 日本語
Yorodumi
- PDB-8p94: Cryo-EM structure of cortactin stabilized Arp2/3-complex nucleate... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8p94
TitleCryo-EM structure of cortactin stabilized Arp2/3-complex nucleated actin branches
Components
  • (Actin-related protein ...) x 7
  • Actin, cytoplasmic 1
  • F-actin-capping protein subunit alpha-1
  • Isoform 2 of F-actin-capping protein subunit beta
  • Phalloidin
  • Src substrate cortactin
KeywordsCONTRACTILE PROTEIN / Complex
Function / homology
Function and homology information


cytoskeletal calyx / regulation of protein kinase C signaling / tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / lamellipodium organization / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle / spindle localization ...cytoskeletal calyx / regulation of protein kinase C signaling / tubulobulbar complex / meiotic chromosome movement towards spindle pole / cytosolic transport / growth cone leading edge / lamellipodium organization / Advanced glycosylation endproduct receptor signaling / RHOF GTPase cycle / spindle localization / meiotic cytokinesis / RHOD GTPase cycle / actin polymerization-dependent cell motility / COPI-independent Golgi-to-ER retrograde traffic / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / muscle cell projection membrane / Gap junction degradation / Formation of annular gap junctions / RHOF GTPase cycle / Clathrin-mediated endocytosis / Formation of the dystrophin-glycoprotein complex (DGC) / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / asymmetric cell division / Arp2/3 protein complex / Arp2/3 complex-mediated actin nucleation / actin nucleation / COPI-mediated anterograde transport / sperm head-tail coupling apparatus / F-actin capping protein complex / WASH complex / Arp2/3 complex binding / mitotic spindle midzone / regulation of cell projection assembly / actin cap / sperm head / modification of postsynaptic actin cytoskeleton / regulation of mitophagy / positive regulation of smooth muscle contraction / profilin binding / Factors involved in megakaryocyte development and platelet production / cellular response to cytochalasin B / regulation of actin filament polymerization / substrate-dependent cell migration, cell extension / regulation of transepithelial transport / positive regulation of chemotaxis / morphogenesis of a polarized epithelium / structural constituent of postsynaptic actin cytoskeleton / cell junction assembly / barbed-end actin filament capping / focal adhesion assembly / protein localization to adherens junction / MHC class II antigen presentation / dense body / actin polymerization or depolymerization / cell projection organization / postsynaptic actin cytoskeleton / Tat protein binding / muscle cell development / proline-rich region binding / regulation of cell morphogenesis / adherens junction assembly / apical protein localization / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / dendritic spine maintenance / podosome / tight junction / lamellipodium assembly / regulation of axon extension / apical junction complex / negative regulation of microtubule polymerization / regulation of norepinephrine uptake / transporter regulator activity / nitric-oxide synthase binding / cortical cytoskeleton / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / filamentous actin / brush border / asymmetric synapse / intercalated disc / kinesin binding / cilium assembly / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / beta-tubulin binding / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / positive regulation of lamellipodium assembly / neuron projection morphogenesis / extrinsic apoptotic signaling pathway / ruffle
Similarity search - Function
Hs1/Cortactin / Repeat in HS1/Cortactin / Cortactin repeat profile. / Cortactin, SH3 domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 ...Hs1/Cortactin / Repeat in HS1/Cortactin / Cortactin repeat profile. / Cortactin, SH3 domain / Actin-related protein 2/3 complex subunit 5 / ARP2/3 complex 16 kDa subunit (p16-Arc) / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 2/3 complex subunit 1 / Arp2/3 complex subunit 2/4 / Actin-related protein 2/3 complex subunit 5 superfamily / Actin-related protein 2/3 complex subunit 3 superfamily / Arp2/3 complex, 34 kD subunit p34-Arc / ARP2/3 complex ARPC3 (21 kDa) subunit / ARP2/3 complex 20 kDa subunit (ARPC4) / 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 / Variant SH3 domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / ATPase, nucleotide binding domain / SH3 domain / WD domain, G-beta repeat / 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
: / ADENOSINE-5'-DIPHOSPHATE / Actin-related protein 2/3 complex subunit 1B / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 3 / Actin-related protein 2 ...: / ADENOSINE-5'-DIPHOSPHATE / Actin-related protein 2/3 complex subunit 1B / Actin-related protein 2/3 complex subunit 2 / Actin-related protein 2/3 complex subunit 3 / F-actin-capping protein subunit alpha-1 / F-actin-capping protein subunit beta / Actin-related protein 2/3 complex subunit 4 / Actin-related protein 3 / Actin-related protein 2 / Src substrate cortactin / Actin, cytoplasmic 1 / Actin-related protein 2/3 complex subunit 5-like protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
Sus scrofa (pig)
Amanita phalloides (death cap)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLiu, T. / Moores, C.A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)810207European Union
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Cortactin stabilizes actin branches by bridging activated Arp2/3 to its nucleated actin filament.
Authors: Tianyang Liu / Luyan Cao / Miroslav Mladenov / Antoine Jegou / Michael Way / Carolyn A Moores /
Abstract: Regulation of the assembly and turnover of branched actin filament networks nucleated by the Arp2/3 complex is essential during many cellular processes, including cell migration and membrane ...Regulation of the assembly and turnover of branched actin filament networks nucleated by the Arp2/3 complex is essential during many cellular processes, including cell migration and membrane trafficking. Cortactin is important for actin branch stabilization, but the mechanism by which this occurs is unclear. Given this, we determined the structure of vertebrate cortactin-stabilized Arp2/3 actin branches using cryogenic electron microscopy. We find that cortactin interacts with the new daughter filament nucleated by the Arp2/3 complex at the branch site, rather than the initial mother actin filament. Cortactin preferentially binds activated Arp3. It also stabilizes the F-actin-like interface of activated Arp3 with the first actin subunit of the new filament, and its central repeats extend along successive daughter-filament subunits. The preference of cortactin for activated Arp3 explains its retention at the actin branch and accounts for its synergy with other nucleation-promoting factors in regulating branched actin network dynamics.
History
DepositionJun 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Feb 7, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3May 29, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Actin-related protein 3
B: Actin-related protein 2
C: Actin-related protein 2/3 complex subunit 1B
D: Actin-related protein 2/3 complex subunit 2
E: Actin-related protein 2/3 complex subunit 3
F: Actin-related protein 2/3 complex subunit 4
G: Actin-related protein 2/3 complex subunit 5-like protein
H: Actin, cytoplasmic 1
I: Src substrate cortactin
J: Actin, cytoplasmic 1
K: Actin, cytoplasmic 1
N: Actin, cytoplasmic 1
O: Actin, cytoplasmic 1
P: Actin, cytoplasmic 1
Q: Actin, cytoplasmic 1
R: Actin, cytoplasmic 1
S: Actin, cytoplasmic 1
U: F-actin-capping protein subunit alpha-1
V: Isoform 2 of F-actin-capping protein subunit beta
W: Actin, cytoplasmic 1
a: Phalloidin
b: Phalloidin
c: Phalloidin
d: Phalloidin
h: Phalloidin
i: Phalloidin
j: Phalloidin
k: Phalloidin
l: Phalloidin
m: Phalloidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)781,19654
Polymers775,77830
Non-polymers5,41824
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Actin-related protein ... , 7 types, 7 molecules ABCDEFG

#1: Protein Actin-related protein 3 / Actin-like protein 3


Mass: 47428.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR3, ARP3 / Production host: unidentified baculovirus / References: UniProt: P61158
#2: Protein Actin-related protein 2 / Actin-like protein 2


Mass: 44818.711 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTR2, ARP2 / Production host: unidentified baculovirus / References: UniProt: P61160
#3: Protein Actin-related protein 2/3 complex subunit 1B / Arp2/3 complex 41 kDa subunit / p41-ARC


Mass: 41004.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC1B, ARC41 / Production host: unidentified baculovirus / References: UniProt: O15143
#4: Protein Actin-related protein 2/3 complex subunit 2 / Arp2/3 complex 34 kDa subunit / p34-ARC


Mass: 34386.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC2, ARC34, PRO2446 / Production host: unidentified baculovirus / References: UniProt: O15144
#5: Protein Actin-related protein 2/3 complex subunit 3 / Arp2/3 complex 21 kDa subunit / p21-ARC


Mass: 20572.666 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC3, ARC21 / Production host: unidentified baculovirus / References: UniProt: O15145
#6: Protein Actin-related protein 2/3 complex subunit 4 / Arp2/3 complex 20 kDa subunit / p20-ARC


Mass: 19697.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC4, ARC20 / Production host: unidentified baculovirus / References: UniProt: P59998
#7: Protein Actin-related protein 2/3 complex subunit 5-like protein / Arp2/3 complex 16 kDa subunit 2 / ARC16-2


Mass: 16964.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARPC5L / Production host: unidentified baculovirus / References: UniProt: Q9BPX5

-
Protein , 4 types, 13 molecules HJKNOPQRSWIUV

#8: Protein
Actin, cytoplasmic 1 / Beta-actin


Mass: 41782.660 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: Q6QAQ1
#9: Protein Src substrate cortactin


Mass: 61340.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cttn, Ems1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q60598
#10: Protein F-actin-capping protein subunit alpha-1 / CapZ alpha-1


Mass: 32980.703 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Capza1, Cappa1 / Production host: Escherichia coli (E. coli) / References: UniProt: P47753
#11: Protein Isoform 2 of F-actin-capping protein subunit beta / CapZ beta


Mass: 30669.768 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Capzb, Cappb1 / Production host: Escherichia coli (E. coli) / References: UniProt: P47757

-
Protein/peptide , 1 types, 10 molecules abcdhijklm

#12: Protein/peptide
Phalloidin


Type: Peptide-like / Class: Toxin / Mass: 808.899 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Amanita phalloides (death cap) / References: BIRD: PRD_002366

-
Non-polymers , 2 types, 24 molecules

#13: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#14: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Cortactin stabilizes Arp2/3-complex nucleated actin branches with daughter filament cappedCOMPLEX#1-#120MULTIPLE SOURCES
2Human Arp2/3 C1BC5L complexCOMPLEX#1-#71RECOMBINANT
3Porcine actin, cytoplasmic 1COMPLEX#81NATURAL
4Mouse cortactinCOMPLEX#91RECOMBINANT
5Mouse capping proteinCOMPLEX#10-#111RECOMBINANT
6PhalloidinCOMPLEX#121NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Sus scrofa (pig)9823
54Mus musculus (house mouse)10090
65Mus musculus (house mouse)10090
76Amanita phalloides (death cap)67723
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21unidentified baculovirus10469
32unidentified baculovirus10469
43unidentified baculovirus10469
54Escherichia coli (E. coli)562
65Escherichia coli (E. coli)562
76Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
Details: 20 mM HEPES pH 7.5, 50mM KCl, 1mM EGTA, 1mM MgCl2, 0.2 mM ATP and 1 mM DTT
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 98 % / Chamber temperature: 295.15 K / Details: Back blotting

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 49.4 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameCategoryFitting-ID
1cryoSPARCparticle selection
3EPUimage acquisition
5cryoSPARCCTF correction
8UCSF ChimeraXmodel fitting1
12ISOLDEmodel refinement1
14ISOLDEmodel refinement2
15Cootmodel refinement2
16cryoSPARCinitial Euler assignment
18cryoSPARCfinal Euler assignment
21cryoSPARC3D reconstruction
CTF correctionDetails: CryoSPARC Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2001580
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 130915 / Symmetry type: POINT
Atomic model building
IDProtocol
1OTHER
2
Atomic model building
ID 3D fitting-IDSource nameType
11AlphaFoldin silico model
22

+
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