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- EMDB-19499: Structure of the F-actin barbed end bound by Cdc12 and profilin (... -

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Entry
Database: EMDB / ID: EMD-19499
TitleStructure of the F-actin barbed end bound by Cdc12 and profilin (ring complex) at a resolution of 6.3 Angstrom
Map dataSharpened cryo-EM density map of the F-actin barbed end bound by Cdc12 and profilin-S71M
Sample
  • Complex: Actin-formin-profilin ring complex: the phalloidin-stabilized F-actin barbed end bound by dimeric-Cdc12 and profilin-S71M.
    • Complex: Actin filamentMicrofilament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Dimeric FH1FH2 domain of S. Pombe Cdc12
      • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,Cell division control protein 12
    • Complex: Profilin-1-S29C/S71M
      • Protein or peptide: Profilin-1
    • Complex: Phalloidin
      • Protein or peptide: Phalloidin (Amanita phalloides)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE IONPhosphate
Keywordsactin / formin / Cdc12 / profilin / 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 / MGMT-mediated DNA damage reversal / medial cortex / mitotic actomyosin contractile ring assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity ...F-bar domain binding / protein localization to mitotic actomyosin contractile ring / medial cortical node / mitotic actomyosin contractile ring, proximal layer / mitotic actomyosin contractile ring / MGMT-mediated DNA damage reversal / medial cortex / mitotic actomyosin contractile ring assembly / methylated-DNA-[protein]-cysteine S-methyltransferase / methylated-DNA-[protein]-cysteine S-methyltransferase activity / positive regulation of norepinephrine uptake / synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / cellular response to cytochalasin B / DNA-methyltransferase activity / 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 / positive regulation of actin filament bundle assembly / Formation of annular gap junctions / GBAF complex / Gap junction degradation / postsynaptic actin cytoskeleton / protein localization to adherens junction / negative regulation of actin filament polymerization / regulation of G0 to G1 transition / dense body / Cell-extracellular matrix interactions / Tat protein binding / DNA alkylation repair / Signaling by ROBO receptors / Folding of actin by CCT/TriC / regulation of double-strand break repair / regulation of actin filament polymerization / DNA ligation / 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 / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / tight junction / positive regulation of ruffle assembly / 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 / negative regulation of stress fiber assembly / 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 actin filament polymerization / positive regulation of stem cell population maintenance / positive regulation of epithelial cell migration / 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 / actin monomer binding / 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 / phosphatidylinositol-4,5-bisphosphate binding / substantia nigra development / actin filament polymerization / phosphotyrosine residue binding / axonogenesis / negative regulation of protein binding / neural tube closure / actin filament
Similarity search - Function
Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Profilin1/2/3, vertebrate / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Methylguanine DNA methyltransferase, ribonuclease-like domain ...Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Profilin1/2/3, vertebrate / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Methylguanine DNA methyltransferase, ribonuclease-like domain / 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / : / Methylated DNA-protein cysteine methyltransferase domain superfamily / Methylated-DNA-[protein]-cysteine S-methyltransferase, active site / Methylated-DNA--protein-cysteine methyltransferase active site. / Profilin conserved 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 / Profilin signature. / Profilin / Profilin / Profilin / Profilin 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 / Armadillo-like helical / Armadillo-type fold / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
Profilin-1 / Methylated-DNA--protein-cysteine methyltransferase / 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: 6.25 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: Science / Year: 2024
Title: Molecular mechanism of actin filament elongation by formins.
Authors: Wout Oosterheert / Micaela Boiero Sanders / Johanna Funk / Daniel Prumbaum / Stefan Raunser / Peter Bieling /
Abstract: Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action ...Formins control the assembly of actin filaments (F-actin) that drive cell morphogenesis and motility in eukaryotes. However, their molecular interaction with F-actin and their mechanism of action remain unclear. In this work, we present high-resolution cryo-electron microscopy structures of F-actin barbed ends bound by three distinct formins, revealing a common asymmetric formin conformation imposed by the filament. Formation of new intersubunit contacts during actin polymerization sterically displaces formin and triggers its translocation. This "undock-and-lock" mechanism explains how actin-filament growth is coordinated with formin movement. Filament elongation speeds are controlled by the positioning and stability of actin-formin interfaces, which distinguish fast and slow formins. Furthermore, we provide a structure of the actin-formin-profilin ring complex, which resolves how profilin is rapidly released from the barbed end during filament elongation.
History
DepositionJan 29, 2024-
Header (metadata) releaseApr 10, 2024-
Map releaseApr 10, 2024-
UpdateApr 24, 2024-
Current statusApr 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19499.png

Downloads & links

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Map

FileDownload / File: emd_19499.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened cryo-EM density map of the F-actin barbed end bound by Cdc12 and profilin-S71M
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.269
Minimum - Maximum-0.34002793 - 1.1353394
Average (Standard dev.)0.0010241653 (±0.033909105)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 422.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19499_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 F-actin...

Fileemd_19499_additional_1.map
Annotation3D-refined, unsharpened cryo-EM density map of the F-actin barbed end bound by Cdc12 and profilin-S71M
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 F-actin barbed...

Fileemd_19499_half_map_1.map
AnnotationUnfiltered half map 2 of the F-actin barbed end bound by Cdc12 and profilin-S71M
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 F-actin barbed...

Fileemd_19499_half_map_2.map
AnnotationUnfiltered half map 1 of the F-actin barbed end bound by Cdc12 and profilin-S71M
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Actin-formin-profilin ring complex: the phalloidin-stabilized F-a...

EntireName: Actin-formin-profilin ring complex: the phalloidin-stabilized F-actin barbed end bound by dimeric-Cdc12 and profilin-S71M.
Components
  • Complex: Actin-formin-profilin ring complex: the phalloidin-stabilized F-actin barbed end bound by dimeric-Cdc12 and profilin-S71M.
    • Complex: Actin filamentMicrofilament
      • Protein or peptide: Actin, cytoplasmic 1, N-terminally processed
    • Complex: Dimeric FH1FH2 domain of S. Pombe Cdc12
      • Protein or peptide: Methylated-DNA--protein-cysteine methyltransferase,Cell division control protein 12
    • Complex: Profilin-1-S29C/S71M
      • Protein or peptide: Profilin-1
    • Complex: Phalloidin
      • Protein or peptide: Phalloidin (Amanita phalloides)
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHATE IONPhosphate

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Supramolecule #1: Actin-formin-profilin ring complex: the phalloidin-stabilized F-a...

SupramoleculeName: Actin-formin-profilin ring complex: the phalloidin-stabilized F-actin barbed end bound by dimeric-Cdc12 and profilin-S71M.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Details: Human beta-actin, human profilin1-S29C/S71M and S. Pombe Cdc12 were purified separately, phalloidin (from Amanita phalloides) was bought from sigma. All components were mixed to assemble the ...Details: Human beta-actin, human profilin1-S29C/S71M 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 FH1FH2 domain of S. Pombe Cdc12

SupramoleculeName: Dimeric FH1FH2 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: Profilin-1-S29C/S71M

SupramoleculeName: Profilin-1-S29C/S71M / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: Phalloidin

SupramoleculeName: Phalloidin / type: complex / ID: 5 / 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: Cytoplasmic beta-actin was recombinantly purified from BTI-Tnao38 cells.
Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.632422 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV THTVPIYEGY ...String:
DDDIAALVVD NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI E(HIC)GIVT NWD DMEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGD GV THTVPIYEGY ALPHAILRLD LAGRDLTDYL MKILTERGYS FTTTAEREIV RDIKEKLCYV ALDFEQEMAT AASSSSLE K SYELPDGQVI TIGNERFRCP EALFQPSFLG MESAGIHETT FNSIMKCDVD IRKDLYANTV LSGGTTMYPG IADRMQKEI TALAPSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDESGP SIVHRKCF

UniProtKB: Actin, cytoplasmic 1

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Macromolecule #2: Methylated-DNA--protein-cysteine methyltransferase,Cell division ...

MacromoleculeName: Methylated-DNA--protein-cysteine methyltransferase,Cell division control protein 12
type: protein_or_peptide / ID: 2
Details: Cdc12(FH1FH2) was purified recombinantly from E. coli with a N-terminal snap-tag.
Number of copies: 2 / Enantiomer: LEVO
EC number: methylated-DNA-[protein]-cysteine S-methyltransferase
Source (natural)Organism: Schizosaccharomyces pombe (fission yeast)
Molecular weightTheoretical: 77.88882 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GAMADKDCEM KRTTLDSPLG KLELSGCEQG LHEIKLLGKG TSAADAVEVP APAAVLGGPE PLMQATAWLN AYFHQPEAIE EFPVPALHH PVFQQESFTR QVLWKLLKVV KFGEVISYQQ LAALAGNPAA TAAVKTALSG NPVPILIPCH RVVSSSGAVG G YEGGLAVK ...String:
GAMADKDCEM KRTTLDSPLG KLELSGCEQG LHEIKLLGKG TSAADAVEVP APAAVLGGPE PLMQATAWLN AYFHQPEAIE EFPVPALHH PVFQQESFTR QVLWKLLKVV KFGEVISYQQ LAALAGNPAA TAAVKTALSG NPVPILIPCH RVVSSSGAVG G YEGGLAVK EWLLAHEGHR LGKPGLGPAG IGAPGSNNSK ITNFDIPNDA TSLPTIITHP TPPPPPPLPV KTSLNTFSHP DS VNIVAND TSVAGVMPAF PPPPPPPPPL VSAAGGKFVS PAVSNNISKD DLHKTTGLTR RPTRRLKQMH WEKLNSGLEF TFW TGPSDE ANKILETLHT SGVLDELDES FAMKEAKTLV KKTCARTDYM SSELQKLFGI HFHKLSHKNP NEIIRMILHC DDSM NECVE FLSSDKVLNQ PKLKADLEPY RIDWANGGDL VNSEKDASEL SRWDYLYVRL IVDLGGYWNQ RMNALKVKNI IETNY ENLV RQTKLIGRAA LELRDSKVFK GLLYLILYLG NYMNDYVRQA KGFAIGSLQR LPLIKNANNT KSLLHILDIT IRKHFP QFD NFSPELSTVT EAAKLNIEAI EQECSELIRG CQNLQIDCDS GALSDPTVFH PDDKILSVIL PWLMEGTKKM DFLKEHL RT MNTTLNNAMR YFGEQPNDPN SKNLFFKRVD SFIIDYSKAR SDNLKSEEEE ASQHRRLNLV N

UniProtKB: Methylated-DNA--protein-cysteine methyltransferase, Cell division control protein 12

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Macromolecule #3: Phalloidin (Amanita phalloides)

MacromoleculeName: Phalloidin (Amanita phalloides) / type: protein_or_peptide / ID: 3 / Details: Phalloidin was bought from sigma. / 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: Profilin-1

MacromoleculeName: Profilin-1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.000207 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AGWNAYIDNL MADGTCQDAA IVGYKDSPCV WAAVPGKTFV NITPAEVGVL VGKDRSSFYV NGLTLGGQKC MVIRDSLLQD GEFSMDLRT KSTGGAPTFN VTVTKTDKTL VLLMGKEGVH GGLINKKCYE MASHLRRSQY

UniProtKB: Profilin-1

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Macromolecule #5: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / 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 #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: PHOSPHATE ION

MacromoleculeName: PHOSPHATE ION / type: ligand / ID: 7 / 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: 3.0 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: 5287 / Average electron dose: 63.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1963686 / Details: Particles picked using SPHIRE-crYOLO.
Startup modelType of model: EMDB MAP
EMDB ID:

19496


Details: Reconstruction of Cdc12 bound to the phalloidin-stabilized F-actin barbed end, in the absence of profilin.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1)
Final 3D classificationNumber classes: 5 / Software - Name: cryoSPARC (ver. v4.2.1)
Details: Masked 3D classification without image alignment in CryoSPARC (5 classes, target resolution 7 Angstrom, initialization mode simple).
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4.2.1)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v4.2.1) / Number images used: 29092
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

8rtt

source_name: PDB, initial_model_type: experimental modelactin-Cdc12-phalloidin model

2pav

source_name: PDB, initial_model_type: experimental modelprofilin model
DetailsRefinement performed using phenix real-space refine
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8rty:
Structure of the F-actin barbed end bound by Cdc12 and profilin (ring complex) at a resolution of 6.3 Angstrom

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