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- PDB-9qfb: Cryo-EM structure of the fully Coronin-1B-decorated actin filamen... -

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Basic information

Entry
Database: PDB / ID: 9qfb
TitleCryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state.
Components
  • Actin, cytoplasmic 1, N-terminally processed
  • Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
KeywordsSTRUCTURAL PROTEIN / actin / coronin / filament / cytoskeleton
Function / homology
Function and homology information


actin filament branching / MGMT-mediated DNA damage reversal / protein localization to cell leading edge / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / Arp2/3 complex binding / negative regulation of smooth muscle cell chemotaxis / regulation of Arp2/3 complex-mediated actin nucleation / positive regulation of norepinephrine uptake / DNA-methyltransferase activity ...actin filament branching / MGMT-mediated DNA damage reversal / protein localization to cell leading edge / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / Arp2/3 complex binding / negative regulation of smooth muscle cell chemotaxis / regulation of Arp2/3 complex-mediated actin nucleation / positive regulation of norepinephrine uptake / DNA-methyltransferase activity / negative regulation of Arp2/3 complex-mediated actin nucleation / endothelial cell chemotaxis / bBAF complex / cellular response to cytochalasin B / npBAF complex / nBAF complex / brahma complex / regulation of transepithelial transport / Formation of annular gap junctions / morphogenesis of a polarized epithelium / Formation of the dystrophin-glycoprotein complex (DGC) / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / protein localization to adherens junction / dense body / postsynaptic actin cytoskeleton / Tat protein binding / ruffle organization / DNA alkylation repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / regulation of double-strand break repair / regulation of nucleotide-excision repair / Adherens junctions interactions / RHOF GTPase cycle / adherens junction assembly / positive regulation of lamellipodium morphogenesis / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / tight junction / 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 / apical junction complex / regulation of norepinephrine uptake / positive regulation of double-strand break repair / transporter regulator activity / maintenance of blood-brain barrier / nitric-oxide synthase binding / cortical cytoskeleton / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / cell leading edge / Regulation of MITF-M-dependent genes involved in pigmentation / Recycling pathway of L1 / brush border / regulation of G1/S transition of mitotic cell cycle / actin filament bundle assembly / kinesin binding / EPH-ephrin mediated repulsion of cells / negative regulation of cell differentiation / RHO GTPases Activate WASPs and WAVEs / regulation of synaptic vesicle endocytosis / positive regulation of myoblast differentiation / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / stress fiber / cellular response to platelet-derived growth factor stimulus / EPHB-mediated forward signaling / cytoskeleton organization / substantia nigra development / axonogenesis / calyx of Held / actin filament organization / nitric-oxide synthase regulator activity / cell periphery / methyltransferase activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / adherens junction / FCGR3A-mediated phagocytosis / actin filament / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / positive regulation of cell differentiation / cell motility / wound healing / RHO GTPases Activate Formins / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / DNA Damage Recognition in GG-NER / Regulation of actin dynamics for phagocytic cup formation / kinetochore / B-WICH complex positively regulates rRNA expression
Similarity search - Function
Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site ...Domain of unknown function DUF1899 / Coronin / Domain of unknown function (DUF1899) / Type of WD40 repeat / DUF1899 / DUF1900 / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding / Methylated DNA-protein cysteine methyltransferase, DNA binding domain / 6-O-methylguanine DNA methyltransferase, DNA binding 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 / ATPase, nucleotide binding domain / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Methylated-DNA--protein-cysteine methyltransferase / Actin, cytoplasmic 1 / Coronin-1B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsOosterheert, W. / Boiero Sanders, M. / Hofnagel, O. / Bieling, P. / Raunser, S.
Funding support Germany, European Union, 4items
OrganizationGrant numberCountry
Max Planck Society Germany
Alexander von Humboldt Foundation Germany
German Research Foundation (DFG)BI 1998/2-1 Germany
European Research Council (ERC)856118European Union
CitationJournal: To Be Published
Title: Choreography of rapid actin filament disassembly by coronin, cofilin and AIP1
Authors: Oosterheert, W. / Boiero Sanders, M. / Hofnagel, O. / Bieling, P. / Raunser, S.
History
DepositionMar 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, cytoplasmic 1, N-terminally processed
B: Actin, cytoplasmic 1, N-terminally processed
C: Actin, cytoplasmic 1, N-terminally processed
D: Actin, cytoplasmic 1, N-terminally processed
E: Actin, cytoplasmic 1, N-terminally processed
F: Actin, cytoplasmic 1, N-terminally processed
G: Actin, cytoplasmic 1, N-terminally processed
H: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
I: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
J: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
K: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
L: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
M: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
N: Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)818,10428
Polymers814,94414
Non-polymers3,16114
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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


Mass: 41632.422 Da / Num. of mol.: 7 / Mutation: C272A
Source method: isolated from a genetically manipulated source
Details: Actin filament. / Source: (gene. exp.) Homo sapiens (human) / Gene: ACTB / Cell line (production host): BTI-Tnao38 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P60709
#2: Protein
Coronin-1B,Methylated-DNA--protein-cysteine methyltransferase / Coronin-2 / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 74788.086 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Details: C-terminal SNAP-tag.,C-terminal SNAP-tag. / Source: (gene. exp.) Homo sapiens (human) / Gene: CORO1B, MGMT / Cell line (production host): BTI-Tnao38 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q9BR76, UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSourceDetails
1Beta-actin filament fully decorated by Coronin-1B.COMPLEX#1-#20RECOMBINANT
2Actin filamentCOMPLEX#11RECOMBINANTAssembled as a double stranded helix of beta-actin subunits.
3Coronin-1BCOMPLEX#21RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Homo sapiens (human)9606
32Homo sapiens (human)9606
43Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
21Trichoplusia ni (cabbage looper)7111BTI-Tnao38
32Trichoplusia ni (cabbage looper)7111BTI-Tnao38
43Trichoplusia ni (cabbage looper)7111BTI-Tnao38
Buffer solutionpH: 7.1
Details: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP, 0.01% Tween20).
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPES1
2100 mMpotassium chlorideKCl1
32 mMmagnesium chlorideMgCl21
41 mMEGTA1
50.5 mMTCEP1
60.01 % (v/v)Tween201
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 R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 286 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm / Cs: 0.01 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 65.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14055
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV
Spherical aberration corrector: The used Titan Krios G2 microscope contains an in-column Cs corrector.

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC4.4particle selectionFilament tracer
2EPUimage acquisition
4cryoSPARC4.4CTF correctionPatch CTF
7Coot0.9.8.1model fitting
8UCSF ChimeraX1.8model fitting
10cryoSPARC4.4initial Euler assignment
11cryoSPARC4.4final Euler assignment
12cryoSPARC4.4classification
13cryoSPARC4.43D reconstructionHelical Refinement
14PHENIX1.21rc1_5015model refinement
CTF correctionDetails: Patch CTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -163.8 ° / Axial rise/subunit: 27.4 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 10071093
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 190940 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Phenix real space refinement.
Atomic model buildingPDB-ID: 9QF2

9qf2


Accession code: 9QF2 / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 81.14 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001542826
ELECTRON MICROSCOPYf_angle_d0.436758184
ELECTRON MICROSCOPYf_chiral_restr0.04296447
ELECTRON MICROSCOPYf_plane_restr0.00337504
ELECTRON MICROSCOPYf_dihedral_angle_d5.85885859

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