[English] 日本語
Yorodumi
- PDB-8cog: Human arginylated beta-actin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cog
TitleHuman arginylated beta-actin
ComponentsActin, cytoplasmic 1, N-terminally processed
KeywordsCONTRACTILE PROTEIN / actin / methylated / filament
Function / homology
Function and homology information


positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport / nBAF complex / brahma complex / morphogenesis of a polarized epithelium / protein localization to adherens junction / postsynaptic actin cytoskeleton ...positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport / nBAF complex / brahma complex / morphogenesis of a polarized epithelium / protein localization to adherens junction / postsynaptic actin cytoskeleton / structural constituent of postsynaptic actin cytoskeleton / Formation of the dystrophin-glycoprotein complex (DGC) / GBAF complex / Formation of annular gap junctions / Tat protein binding / regulation of G0 to G1 transition / Gap junction degradation / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / regulation of nucleotide-excision repair / regulation of double-strand break repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / apical protein localization / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / regulation of norepinephrine uptake / transporter regulator activity / apical junction complex / nitric-oxide synthase binding / positive regulation of double-strand break repair / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / establishment or maintenance of cell polarity / cortical cytoskeleton / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of synaptic vesicle endocytosis / Recycling pathway of L1 / regulation of G1/S transition of mitotic cell cycle / brush border / kinesin binding / negative regulation of cell differentiation / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / cytoskeleton organization / EPHB-mediated forward signaling / substantia nigra development / calyx of Held / axonogenesis / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / adherens junction / positive regulation of cell differentiation / actin filament / FCGR3A-mediated phagocytosis / cell motility / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / Schaffer collateral - CA1 synapse / B-WICH complex positively regulates rRNA expression / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / kinetochore / Regulation of actin dynamics for phagocytic cup formation / structural constituent of cytoskeleton / tau protein binding / VEGFA-VEGFR2 Pathway / platelet aggregation / cytoplasmic ribonucleoprotein granule / nuclear matrix / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / UCH proteinases / Signaling by BRAF and RAF1 fusions / nucleosome / cell-cell junction / lamellipodium / actin cytoskeleton / presynapse / Clathrin-mediated endocytosis / HATs acetylate histones / Factors involved in megakaryocyte development and platelet production / regulation of apoptotic process
Similarity search - Function
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
ADENOSINE-5'-DIPHOSPHATE / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.499 Å
AuthorsPinto, C.S. / Bakker, S.E. / Suchenko, A. / Hussain, H. / Hatano, T. / Sampath, K. / Chinthalapudi, K. / Mishima, M. / Balasubramanian, M.
Funding support United Kingdom, European Union, 4items
OrganizationGrant numberCountry
Wellcome TrustWT101885MA United Kingdom
European Research Council (ERC)671083-ACTOMYOSIN RINGEuropean Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S003789/1 United Kingdom
Wellcome Trust203276/Z/16/Z United Kingdom
CitationJournal: To Be Published
Title: Structure and physiological investigation of human arginylated beta-actin
Authors: Pinto, C.S. / Bakker, S.E. / Suchenko, A. / Hussain, H. / Hatano, T. / Sampath, K. / Chinthalapudi, K. / Mishima, M. / Balasubramanian, M.
History
DepositionFeb 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Actin, cytoplasmic 1, N-terminally processed
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1583
Polymers41,7071
Non-polymers4522
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1000 Å2
ΔGint-19 kcal/mol
Surface area16660 Å2

-
Components

#1: Protein Actin, cytoplasmic 1, N-terminally processed


Mass: 41706.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Production host: Komagataella pastoris (fungus) / References: UniProt: P60709
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Polymerised arginylated actin with bound ADP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 7.4
Details: Actin for EM was polymerized by mixing, 20 ul 20 uM G-actin, 8 ul 10x MKE and 52 ul 5 mM HEPES-KOH pH 7.4 containing 0.2 mM ATP and 0.5 mM DTT and incubating at RT for 1 hour.
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

-
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: 75000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 700 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 60 sec. / Electron dose: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1

-
Processing

SoftwareName: REFMAC / Version: 5.8.0267 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk / Date: 2020-24-08
Description: (un)restrained refinement or idealisation of macromolecular structures
EM software
IDNameVersionCategoryDetails
1RELION3.09particle selection
4RELIONCTF correction
7Cootmodel fitting
9REFMACmodel refinementServalcat
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.499 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42701 / Algorithm: FOURIER SPACE
Details: RELION 3.09 was used throughout using helical reconstruction.
Symmetry type: POINT
RefinementResolution: 3.499→3.499 Å / Cor.coef. Fo:Fc: 0.806 / WRfactor Rwork: 0.36 / SU B: 20.983 / SU ML: 0.319 / Average fsc overall: 0.8232 / Average fsc work: 0.8232 / ESU R: 0.508
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rwork0.3599 28866 -
all0.36 --
Rfree--0 %
obs--100 %
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso mean: 77.447 Å2
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.0133012
ELECTRON MICROSCOPYr_bond_other_d0.0010.0172823
ELECTRON MICROSCOPYr_angle_refined_deg1.6351.6484086
ELECTRON MICROSCOPYr_angle_other_deg1.3421.5766524
ELECTRON MICROSCOPYr_dihedral_angle_1_deg7.0485373
ELECTRON MICROSCOPYr_dihedral_angle_2_deg36.52822.109147
ELECTRON MICROSCOPYr_dihedral_angle_3_deg17.59415517
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.9071519
ELECTRON MICROSCOPYr_chiral_restr0.0710.2405
ELECTRON MICROSCOPYr_gen_planes_refined0.0070.023368
ELECTRON MICROSCOPYr_gen_planes_other0.0030.02662
ELECTRON MICROSCOPYr_nbd_refined0.210.21446
ELECTRON MICROSCOPYr_symmetry_nbd_other0.1930.25716
ELECTRON MICROSCOPYr_nbtor_refined0.1660.22990
ELECTRON MICROSCOPYr_symmetry_nbtor_other0.0770.23152
ELECTRON MICROSCOPYr_xyhbond_nbd_refined0.1550.2122
ELECTRON MICROSCOPYr_symmetry_xyhbond_nbd_other0.060.24
ELECTRON MICROSCOPYr_mcbond_it10.3477.2151494
ELECTRON MICROSCOPYr_mcbond_other10.3457.2151494
ELECTRON MICROSCOPYr_mcangle_it17.08810.8061866
ELECTRON MICROSCOPYr_mcangle_other17.08510.8191867
ELECTRON MICROSCOPYr_scbond_it12.8348.9541518
ELECTRON MICROSCOPYr_scbond_other12.8348.9541518
ELECTRON MICROSCOPYr_scangle_it21.72612.6972220
ELECTRON MICROSCOPYr_scangle_other21.72112.6932221
ELECTRON MICROSCOPYr_lrange_it36.106140.25312140
ELECTRON MICROSCOPYr_lrange_other36.105140.24312141
LS refinement shell

Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %

Resolution (Å)Rfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc workWRfactor Rwork
3.4-3.4881.03621231.03621230.491.036
3.488-3.5840.6520780.6520780.6070.65
3.584-3.6870.47620070.47620070.7010.476
3.687-3.8010.43819500.43819500.7420.438
3.801-3.9250.38418850.38418850.8060.384
3.925-4.0630.32818820.32818820.8570.328
4.063-4.2160.29918110.29918110.8910.299
4.216-4.3870.29916350.29916350.9150.299
4.387-4.5820.31316840.31316840.9330.313
4.582-4.8050.31715670.31715670.9410.317
4.805-5.0640.30514890.30514890.9420.305
5.064-5.370.29914210.29914210.9290.299
5.37-5.7390.28513320.28513320.9110.285
5.739-6.1970.28512470.28512470.8970.285
6.197-6.7850.30211330.30211330.8830.302
6.785-7.580.32510390.32510390.8760.325
7.58-8.7420.3078940.3078940.8730.307
8.742-10.6810.2637410.2637410.9050.263
10.681-14.9970.2616100.2616100.9420.261
14.997-88.560.7783380.7783380.9780.778

+
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