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- PDB-9qfw: Cryo-EM structure of the cofilactin barbed end bound by two AIP1 ... -

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Basic information

Entry
Database: PDB / ID: 9qfw
TitleCryo-EM structure of the cofilactin barbed end bound by two AIP1 molecules
Components
  • Actin, cytoplasmic 1, N-terminally processed
  • Cofilin-1
  • WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase
KeywordsSTRUCTURAL PROTEIN / actin / cofilin / AIP1 / barbed end / filament / cytoskeleton
Function / homology
Function and homology information


establishment of planar polarity of follicular epithelium / regulation of actin filament depolymerization / regulation of oligodendrocyte differentiation / MGMT-mediated DNA damage reversal / cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping ...establishment of planar polarity of follicular epithelium / regulation of actin filament depolymerization / regulation of oligodendrocyte differentiation / MGMT-mediated DNA damage reversal / cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / neural fold formation / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / maintenance of epithelial cell apical/basal polarity / positive regulation of actin filament depolymerization / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / positive regulation of embryonic development / DNA-methyltransferase activity / negative regulation of actin filament bundle assembly / positive regulation of synaptic plasticity / negative regulation of actin filament depolymerization / bBAF complex / cellular response to cytochalasin B / npBAF complex / neutrophil migration / cortical cytoskeleton organization / nBAF complex / brahma complex / actin filament severing / 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 / apical junction assembly / Gap junction degradation / regulation of G0 to G1 transition / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / regulation of dendritic spine morphogenesis / protein localization to adherens junction / establishment of spindle localization / host-mediated activation of viral process / actin filament depolymerization / dense body / cell projection organization / postsynaptic actin cytoskeleton / Tat protein binding / regulation of ventricular cardiac muscle cell membrane repolarization / negative regulation of cell adhesion / negative regulation of cell motility / DNA alkylation repair / RHO GTPases Activate ROCKs / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / locomotion / negative regulation of cell size / regulation of double-strand break repair / regulation of nucleotide-excision repair / cellular response to interleukin-6 / neutrophil mediated immunity / regulation of cell morphogenesis / Adherens junctions interactions / negative regulation of dendritic spine maintenance / RHOF GTPase cycle / adherens junction assembly / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / neural crest cell migration / Interaction between L1 and Ankyrins / podosome / tight junction / platelet formation / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / sarcomere organization / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of cell motility / positive regulation of T cell differentiation / apical junction complex / cortical actin cytoskeleton / phosphatidylinositol bisphosphate binding / cellular response to insulin-like growth factor stimulus / regulation of norepinephrine uptake / positive regulation of double-strand break repair / transporter regulator activity / maintenance of blood-brain barrier / establishment of cell polarity / nitric-oxide synthase binding / positive regulation of dendritic spine development / cortical cytoskeleton / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation
Similarity search - Function
Nitrous oxide reductase, N-terminal / ADF/Cofilin / 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 ...Nitrous oxide reductase, N-terminal / ADF/Cofilin / 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 / 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 / WD domain, G-beta repeat / G-protein beta WD-40 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 / WD repeat-containing protein 1 / Methylated-DNA--protein-cysteine methyltransferase / Cofilin-1 / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 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 12, 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: Cofilin-1
G: Cofilin-1
H: Cofilin-1
I: Cofilin-1
J: Cofilin-1
P: WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase
Q: WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)476,60422
Polymers474,34712
Non-polymers2,25810
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.: 5 / Mutation: C272A
Source method: isolated from a genetically manipulated source
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
Cofilin-1 / 18 kDa phosphoprotein / p18 / Cofilin / non-muscle isoform


Mass: 18532.531 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P23528
#3: Protein WD repeat-containing protein 1,Methylated-DNA--protein-cysteine methyltransferase / Actin-interacting protein 1 / AIP1 / NORI-1 / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6- ...Actin-interacting protein 1 / AIP1 / NORI-1 / 6-O-methylguanine-DNA methyltransferase / MGMT / O-6-methylguanine-DNA-alkyltransferase


Mass: 86760.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: AIP1 has a C-terminal SNAP tag,AIP1 has a C-terminal SNAP tag
Source: (gene. exp.) Homo sapiens (human) / Gene: WDR1, MGMT / Cell line (production host): BTI-Tnao38 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: O75083, UniProt: P16455, methylated-DNA-[protein]-cysteine S-methyltransferase
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
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: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Cofilactin barbed end bound by two AIP1 moleculesCOMPLEXBarbed end of the actin filament fully decorated by Cofilin-1 and bound by two AIP1 molecules#1-#30MULTIPLE SOURCES
2Actin filamentCOMPLEX#11RECOMBINANT
3Cofilin-1COMPLEX#21RECOMBINANT
4AIP1COMPLEX#31RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22NO
31NO
44
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
11Trichoplusia ni (cabbage looper)7111
22Trichoplusia ni (cabbage looper)7111
33Escherichia coli BL21(DE3) (bacteria)469008
44Trichoplusia ni (cabbage looper)7111
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, 0.015% Tween20)
Buffer component
IDConc.NameBuffer-ID
110 mMHEPES1
2100 mMpotassium chloride1
32 mMmagnesium chloride1
41 mMEGTA1
50.5 mMTCEP1
60.015 % (v/v)Tween201
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / 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 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: 71.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 23082
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 15 eV
Spherical aberration corrector: Data were collected using a 300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) equipped with an in-column Cs corrector

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Processing

EM software
IDNameVersionCategoryDetails
1crYOLO1.9particle selection
2EPUimage acquisition
4cryoSPARC4.4CTF correctionPatch CTF
7UCSF ChimeraX1.8model fitting
8Coot0.9.8.1model fitting
10PHENIX1.21rc1_5015model refinement
11cryoSPARC4.4initial Euler assignment
12cryoSPARC4.4final Euler assignment
13cryoSPARC4.4classification
14cryoSPARC4.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3916837
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23577 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Details: Phenix real space refinement
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
19QFJ

9qfj

19QFJ1PDBexperimental model
21O750832AlphaFoldin silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 106.48 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002130386
ELECTRON MICROSCOPYf_angle_d0.503441135
ELECTRON MICROSCOPYf_chiral_restr0.04434579
ELECTRON MICROSCOPYf_plane_restr0.00335237
ELECTRON MICROSCOPYf_dihedral_angle_d8.47724159

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