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- EMDB-19496: Structure of the formin Cdc12 bound to the barbed end of phalloid... -

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Entry
Database: EMDB / ID: EMD-19496
TitleStructure of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin.
Map dataSharpened, local-resolution filtered cryo-EM density map of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin.
Sample
  • Complex: Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the barbed end of phalloidin stabilized F-actin.
    • Complex: Actin filamentMicrofilament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Dimeric FH2 domain of S. Pombe Cdc12
      • Protein or peptide: Cell division control protein 12
    • Complex: Phalloidin.
      • Protein or peptide: Phalloidin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE IONPhosphate
Keywordsactin / formin / Cdc12 / actin assembly. / STRUCTURAL PROTEIN
Function / homology
Function and homology information


F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex ...F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / mitotic actomyosin contractile ring / medial cortex / mitotic actomyosin contractile ring assembly / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / bBAF complex / npBAF complex / postsynaptic actin cytoskeleton organization / regulation of transepithelial transport / brahma complex / nBAF complex / structural constituent of postsynaptic actin cytoskeleton / morphogenesis of a polarized epithelium / Formation of annular gap junctions / GBAF complex / Gap junction degradation / postsynaptic actin cytoskeleton / protein localization to adherens junction / regulation of G0 to G1 transition / dense body / Cell-extracellular matrix interactions / Tat protein binding / Folding of actin by CCT/TriC / regulation of double-strand break repair / regulation of nucleotide-excision repair / RSC-type complex / apical protein localization / mating projection tip / Prefoldin mediated transfer of substrate to CCT/TriC / barbed-end actin filament capping / adherens junction assembly / RHOF GTPase cycle / Adherens junctions interactions / tight junction / Sensory processing of sound by outer hair cells of the cochlea / SWI/SNF complex / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / regulation of norepinephrine uptake / positive regulation of double-strand break repair / positive regulation of T cell differentiation / NuA4 histone acetyltransferase complex / regulation of synaptic vesicle endocytosis / apical junction complex / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / cell division site / cortical cytoskeleton / positive regulation of double-strand break repair via homologous recombination / positive regulation of stem cell population maintenance / nitric-oxide synthase binding / Recycling pathway of L1 / regulation of cyclin-dependent protein serine/threonine kinase activity / regulation of G1/S transition of mitotic cell cycle / actin filament bundle assembly / negative regulation of cell differentiation / brush border / kinesin binding / calyx of Held / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / regulation of protein localization to plasma membrane / EPHB-mediated forward signaling / substantia nigra development / actin filament polymerization / axonogenesis / negative regulation of protein binding / actin filament / cell motility / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of transmembrane transporter activity / positive regulation of cell differentiation / FCGR3A-mediated phagocytosis / adherens junction / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA Damage Recognition in GG-NER / tau protein binding / Signaling by high-kinase activity BRAF mutants / Schaffer collateral - CA1 synapse / MAP2K and MAPK activation / B-WICH complex positively regulates rRNA expression / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / kinetochore / Regulation of actin dynamics for phagocytic cup formation / platelet aggregation / small GTPase binding / nuclear matrix / VEGFA-VEGFR2 Pathway / UCH proteinases / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants
Similarity search - Function
Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily ...Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Actin, cytoplasmic 1 / Cell division control protein 12
Similarity search - Component
Biological speciesHomo sapiens (human) / Schizosaccharomyces pombe (fission yeast) / Amanita phalloides (death cap)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.56 Å
AuthorsOosterheert W / Boiero Sanders M / Funk J / Prumbaum D / Raunser S / Bieling P
Funding support Germany, European Union, 3 items
OrganizationGrant numberCountry
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: Mechanism of formin-mediated processive elongation of actin filaments revealed by cryo-EM
Authors: Oosterheert W / Boiero Sanders M / Funk J / Prumbaum D / Raunser S / Bieling P
History
DepositionJan 29, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 10, 2024-
Current statusApr 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19496.png

Downloads & links

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Map

FileDownload / File: emd_19496.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened, local-resolution filtered cryo-EM density map of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin.
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.0272
Minimum - Maximum-0.08265745 - 0.18338019
Average (Standard dev.)0.00025321 (±0.0048892903)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 281.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19496_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: 3D-refined, unsharpened cryo-EM density map of the formin...

Fileemd_19496_additional_1.map
Annotation3D-refined, unsharpened cryo-EM density map of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened cryo-EM density map of actin-Cdc12. This reconstruction...

Fileemd_19496_additional_2.map
AnnotationUnsharpened cryo-EM density map of actin-Cdc12. This reconstruction was computed with more particles, but displays weaker density for the FH2L domain of Cdc12 due to flexibility.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Composite map of two reconstructions of the formin...

Fileemd_19496_additional_3.map
AnnotationComposite map of two reconstructions of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin. This map was created using phenix and was used for visualization purposes.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unfiltered half map 1 of actin-Cdc12. This reconstruction...

Fileemd_19496_additional_4.map
AnnotationUnfiltered half map 1 of actin-Cdc12. This reconstruction was computed with more particles, but displays weaker density for the FH2L domain of Cdc12 due to flexibility.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unfiltered half map 2 of actin-Cdc12. This reconstruction...

Fileemd_19496_additional_5.map
AnnotationUnfiltered half map 2 of actin-Cdc12. This reconstruction was computed with more particles, but displays weaker density for the FH2L domain of Cdc12 due to flexibility.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened density map of actin-Cdc12. This reconstruction was...

Fileemd_19496_additional_6.map
AnnotationSharpened density map of actin-Cdc12. This reconstruction was computed with more particles, but displays weaker density for the FH2L domain of Cdc12 due to flexibility.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 1 of the formin Cdc12...

Fileemd_19496_half_map_1.map
AnnotationUnfiltered half map 1 of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered half map 2 of the formin Cdc12...

Fileemd_19496_half_map_2.map
AnnotationUnfiltered half map 2 of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the ...

EntireName: Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the barbed end of phalloidin stabilized F-actin.
Components
  • Complex: Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the barbed end of phalloidin stabilized F-actin.
    • Complex: Actin filamentMicrofilament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Dimeric FH2 domain of S. Pombe Cdc12
      • Protein or peptide: Cell division control protein 12
    • Complex: Phalloidin.
      • Protein or peptide: Phalloidin
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE IONPhosphate

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Supramolecule #1: Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the ...

SupramoleculeName: Complex of the dimeric FH2 domain of S. Pombe Cdc12 bound to the barbed end of phalloidin stabilized F-actin.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Details: Human beta-actin and S. Pombe Cdc12 were purified separately, phalloidin (from Amanita phalloides) was bought from sigma. All components were mixed to assemble the complex prior to cryo-EM grid preparation.

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Supramolecule #2: Actin filament

SupramoleculeName: Actin filament / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Dimeric FH2 domain of S. Pombe Cdc12

SupramoleculeName: Dimeric FH2 domain of S. Pombe Cdc12 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)

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Supramolecule #4: Phalloidin.

SupramoleculeName: Phalloidin. / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3 / Details: Stabilizes the actin filament.
Source (natural)Organism: Amanita phalloides (death cap)

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

MacromoleculeName: Actin, cytoplasmic 1, N-terminally processed / type: protein_or_peptide / ID: 1
Details: Recombinant beta-actin purified from BTI-Tnao38 cells.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.763617 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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 GMESAGIHET TFNSIMKCDV DIRKDLYANT VLSGGTTMYP GIADRMQKE ITALAPSTMK IKIIAPPERK YSVWIGGSIL ASLSTFQQMW ISKQEYDESG PSIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #2: Cell division control protein 12

MacromoleculeName: Cell division control protein 12 / type: protein_or_peptide / ID: 2
Details: FH2 domain of S. pombe Cdc12, purified from E. coli cells.
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 48.495242 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SKDDLHKTTG LTRRPTRRLK QMHWEKLNSG LEFTFWTGPS DEANKILETL HTSGVLDELD ESFAMKEAKT LVKKTCARTD YMSSELQKL FGIHFHKLSH KNPNEIIRMI LHCDDSMNEC VEFLSSDKVL NQPKLKADLE PYRIDWANGG DLVNSEKDAS E LSRWDYLY ...String:
SKDDLHKTTG LTRRPTRRLK QMHWEKLNSG LEFTFWTGPS DEANKILETL HTSGVLDELD ESFAMKEAKT LVKKTCARTD YMSSELQKL FGIHFHKLSH KNPNEIIRMI LHCDDSMNEC VEFLSSDKVL NQPKLKADLE PYRIDWANGG DLVNSEKDAS E LSRWDYLY VRLIVDLGGY WNQRMNALKV KNIIETNYEN LVRQTKLIGR AALELRDSKV FKGLLYLILY LGNYMNDYVR QA KGFAIGS LQRLPLIKNA NNTKSLLHIL DITIRKHFPQ FDNFSPELST VTEAAKLNIE AIEQECSELI RGCQNLQIDC DSG ALSDPT VFHPDDKILS VILPWLMEGT KKMDFLKEHL RTMNTTLNNA MRYFGEQPND PNSKNLFFKR VDSFIIDYSK ARSD NLKSE EEEASQHRRL NLVN

UniProtKB: Cell division control protein 12

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Macromolecule #3: Phalloidin

MacromoleculeName: Phalloidin / type: protein_or_peptide / ID: 3 / Details: phalloidin, purified from Amanita phalloides. / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Amanita phalloides (death cap)
Molecular weightTheoretical: 808.899 Da
SequenceString:
W(EEP)A(DTH)C(HYP)A

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: PO4
Molecular weightTheoretical: 94.971 Da
Chemical component information

ChemComp-PO4:
PHOSPHATE ION / Phosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.1
Component:
ConcentrationNameFormula
10.0 mMHEPES
100.0 mMsodium chlorideNaClSodium chloride
2.0 mMmagnesium chlorideMgCl2
1.0 mMEGTA
0.5 mMTCEP

Details: 1xKMEH (10 mM HEPES pH 7.1, 100 mM KCl, 2 mM MgCl2, 1 mM EGTA, 0.5 mM TCEP)
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 286 K / Instrument: FEI VITROBOT MARK IV / Details: 3 seconds, force 0..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 0.01 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Specialist opticsSpherical aberration corrector: Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector.
Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV / Details: Gatan energy filter.
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Details300 kV Titan Krios G2 microscope (Thermo Fisher Scientific) with an in-column Cs-corrector.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 20393 / Average electron dose: 64.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5200600 / Details: Particles picked using SPHIRE-crYOLO.
Startup modelType of model: NONE / Details: Ab initio reconstruction in cryosparc.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.3.2)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.1.0) / Details: 3D classification in RELION.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.0) / Details: Refinement performed in RELION. / Number images used: 154570
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8a2s

chain_id: C, source_name: PDB, initial_model_type: experimental modelactin model
source_name: AlphaFold, initial_model_type: in silico modelCdc12 model

6t1y

source_name: PDB, initial_model_type: experimental modelphalloidin model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8rtt:
Structure of the formin Cdc12 bound to the barbed end of phalloidin-stabilized F-actin.

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