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- EMDB-41667: Cryo-EM structure of the PP2A:B55-FAM122A complex, B55 body -

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Entry
Database: EMDB / ID: EMD-41667
TitleCryo-EM structure of the PP2A:B55-FAM122A complex, B55 body
Map dataRelion multi-body refinement, B55 body, full map
Sample
  • Complex: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to FAM122A
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
    • Protein or peptide: PPP2R1A-PPP2R2A-interacting phosphatase regulator 1
KeywordsProtein Phosphatase 2A:B55 holoenzyme FAM122A inhibitor substrate binding cell cycle regulation / SIGNALING PROTEIN
Function / homology
Function and homology information


protein serine/threonine phosphatase inhibitor activity / regulation of chromosome segregation / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex ...protein serine/threonine phosphatase inhibitor activity / regulation of chromosome segregation / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation / mitotic sister chromatid separation / meiotic sister chromatid cohesion, centromeric / INTAC complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein phosphatase regulator activity / GABA receptor binding / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / protein antigen binding / ERKs are inactivated / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Initiation of Nuclear Envelope (NE) Reformation / mitotic G2/M transition checkpoint / RNA polymerase II transcription initiation surveillance / Co-stimulation by CD28 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of epithelial to mesenchymal transition / response to morphine / Co-inhibition by CTLA4 / protein phosphatase inhibitor activity / Platelet sensitization by LDL / protein-serine/threonine phosphatase / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / ERK/MAPK targets / mesoderm development / protein serine/threonine phosphatase activity / vascular endothelial cell response to oscillatory fluid shear stress / T cell homeostasis / regulation of cell differentiation / phosphoprotein phosphatase activity / regulation of microtubule polymerization / regulation of G1/S transition of mitotic cell cycle / lateral plasma membrane / chromosome, centromeric region / DARPP-32 events / enzyme-substrate adaptor activity / negative regulation of hippo signaling / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein dephosphorylation / Cyclin A/B1/B2 associated events during G2/M transition / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein tyrosine phosphatase activity / Resolution of Sister Chromatid Cohesion / protein phosphatase 2A binding / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AURKA Activation by TPX2 / meiotic cell cycle / chromosome segregation / RHO GTPases Activate Formins / RAF activation / Spry regulation of FGF signaling / negative regulation of canonical Wnt signaling pathway / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / response to lead ion / tau protein binding / spindle pole / Negative regulation of MAPK pathway / Cyclin D associated events in G1 / Separation of Sister Chromatids / Regulation of TP53 Degradation / Regulation of PLK1 Activity at G2/M Transition / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / microtubule cytoskeleton / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling
Similarity search - Function
PABIR1/2/3 / Protein phosphatase 2A regulatory subunit PR55 / Protein phosphatase 2A regulatory subunit PR55, conserved site / Protein phosphatase 2A regulatory subunit PR55 signature 1. / Protein phosphatase 2A regulatory subunit PR55 signature 2. / : / : / HEAT repeat / HEAT repeat / : ...PABIR1/2/3 / Protein phosphatase 2A regulatory subunit PR55 / Protein phosphatase 2A regulatory subunit PR55, conserved site / Protein phosphatase 2A regulatory subunit PR55 signature 1. / Protein phosphatase 2A regulatory subunit PR55 signature 2. / : / : / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / HEAT repeat profile. / HEAT, type 2 / HEAT repeats / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Armadillo-like helical / Armadillo-type fold / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PPP2R1A-PPP2R2A-interacting phosphatase regulator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsFuller JR / Padi SKR / Peti W / Page R
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144379 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM134683 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS124666 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: Real-space refinement in PHENIX for cryo-EM and crystallography.
Authors: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams /
Abstract: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps.
History
DepositionAug 21, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41667.png

Downloads & links

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Map

FileDownload / File: emd_41667.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRelion multi-body refinement, B55 body, full map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.53 Å/pix.
x 540 pix.
= 288.36 Å		0.53 Å/pix.
x 540 pix.
= 288.36 Å		0.53 Å/pix.
x 540 pix.
= 288.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.534 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.003
Minimum - Maximum-0.005153373 - 0.013365378
Average (Standard dev.)-0.000009703317 (±0.0002537485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 288.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_41667_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Map sharpened by an automatically-determined B-factor (-52.9654) and...

Fileemd_41667_additional_1.map
AnnotationMap sharpened by an automatically-determined B-factor (-52.9654) and filtered to local resolution by the Relion locres implementation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Relion multi-body refinement, B55 body, half map 1

Fileemd_41667_half_map_1.map
AnnotationRelion multi-body refinement, B55 body, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Relion multi-body refinement, B55 body, half map 2

Fileemd_41667_half_map_2.map
AnnotationRelion multi-body refinement, B55 body, half map 2
Projections & Slices
AxesZYX

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Sample components

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Entire : Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to FAM122A

EntireName: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to FAM122A
Components
  • Complex: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to FAM122A
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
    • Protein or peptide: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
    • Protein or peptide: PPP2R1A-PPP2R2A-interacting phosphatase regulator 1

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Supramolecule #1: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to FAM122A

SupramoleculeName: Quadruple complex of PP2A:B55 (PP2Aa:PP2Ac:B55) bound to FAM122A
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.95798 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GHMSLYPIAV LIDELRNEDV QLRLNSIKKL STIALALGVE RTRSELLPFL TDTIYDEDEV LLALAEQLGT FTTLVGGPEY VHCLLPPLE SLATVEETVV RDKAVESLRA ISHEHSPSDL EAHFVPLVKR LAGGDWFTSR TSACGLFSVC YPRVSSAVKA E LRQYFRNL ...String:
GHMSLYPIAV LIDELRNEDV QLRLNSIKKL STIALALGVE RTRSELLPFL TDTIYDEDEV LLALAEQLGT FTTLVGGPEY VHCLLPPLE SLATVEETVV RDKAVESLRA ISHEHSPSDL EAHFVPLVKR LAGGDWFTSR TSACGLFSVC YPRVSSAVKA E LRQYFRNL CSDDTPMVRR AAASKLGEFA KVLELDNVKS EIIPMFSNLA SDEQDSVRLL AVEACVNIAQ LLPQEDLEAL VM PTLRQAA EDKSWRVRYM VADKFTELQK AVGPEITKTD LVPAFQNLMK DCEAEVRAAA SHKVKEFCEN LSADCRENVI MSQ ILPCIK ELVSDANQHV KSALASVIMG LSPILGKDNT IEHLLPLFLA QLKDECPEVR LNIISNLDCV NEVIGIRQLS QSLL PAIVE LAEDAKWRVR LAIIEYMPLL AGQLGVEFFD EKLNSLCMAW LVDHVYAIRE AATSNLKKLV EKFGKEWAHA TIIPK VLAM SGDPNYLHRM TTLFCINVLS EVCGQDITTK HMLPTVLRMA GDPVANVRFN VAKSLQKIGP ILDNSTLQSE VKPILE KLT QDQDVDVKYF AQEALTVLSL A

UniProtKB: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

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Macromolecule #2: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit...

MacromoleculeName: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.10134 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GHMGSAGAGG GNDIQWCFSQ VKGAVDDDVA EADIISTVEF NHSGELLATG DKGGRVVIFQ QEQENKIQSH SRGEYNVYST FQSHEPEFD YLKSLEIEEK INKIRWLPQK NAAQFLLSTN DKTIKLWKIS ERDKRPEGYN LKEEDGRYRD PTTVTTLRVP V FRPMDLMV ...String:
GHMGSAGAGG GNDIQWCFSQ VKGAVDDDVA EADIISTVEF NHSGELLATG DKGGRVVIFQ QEQENKIQSH SRGEYNVYST FQSHEPEFD YLKSLEIEEK INKIRWLPQK NAAQFLLSTN DKTIKLWKIS ERDKRPEGYN LKEEDGRYRD PTTVTTLRVP V FRPMDLMV EASPRRIFAN AHTYHINSIS INSDYETYLS ADDLRINLWH LEITDRSFNI VDIKPANMEE LTEVITAAEF HP NSCNTFV YSSSKGTIRL CDMRASALCD RHSKLFEEPE DPSNRSFFSE IISSISDVKF SHSGRYMMTR DYLSVKIWDL NME NRPVET YQVHEYLRSK LCSLYENDCI FDKFECCWNG SDSVVMTGSY NNFFRMFDRN TKRDITLEAS RENNKPRTVL KPRK VCASG KRKKDEISVD SLDFNKKILH TAWHPKENII AVATTNNLYI FQDKVN

UniProtKB: Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform

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Macromolecule #3: Serine/threonine-protein phosphatase 2A catalytic subunit alpha i...

MacromoleculeName: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein-serine/threonine phosphatase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.845375 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GHMDEKVFTK ELDQWIEQLN ECKQLSESQV KSLCEKAKEI LTKESNVQEV RCPVTVCGDV HGQFHDLMEL FRIGGKSPDT NYLFMGDYV DRGYYSVETV TLLVALKVRY RERITILRGN HESRQITQVY GFYDECLRKY GNANVWKYFT DLFDYLPLTA L VDGQIFCL ...String:
GHMDEKVFTK ELDQWIEQLN ECKQLSESQV KSLCEKAKEI LTKESNVQEV RCPVTVCGDV HGQFHDLMEL FRIGGKSPDT NYLFMGDYV DRGYYSVETV TLLVALKVRY RERITILRGN HESRQITQVY GFYDECLRKY GNANVWKYFT DLFDYLPLTA L VDGQIFCL HGGLSPSIDT LDHIRALDRL QEVPHEGPMC DLLWSDPDDR GGWGISPRGA GYTFGQDISE TFNHANGLTL VS RAHQLVM EGYNWCHDRN VVTIFSAPNY CYRCGNQAAI MELDDTLKYS FLQFDPAPRR GEPHVTRRTP DYF(MLL)

UniProtKB: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform

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Macromolecule #4: PPP2R1A-PPP2R2A-interacting phosphatase regulator 1

MacromoleculeName: PPP2R1A-PPP2R2A-interacting phosphatase regulator 1 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.680907 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GHMGGGLRRS NSAPLIHGLS DSSPVFQDEA PSARRNRTTF PSRHGLLLPA SPVRMHSSRL HQIKQEEGMD LINRETVHER EVQTAMQIS HSWEES

UniProtKB: PPP2R1A-PPP2R2A-interacting phosphatase regulator 1

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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

Concentration1.2 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
1.0 mMMnCl2manganese (II) chloride
20.0 mMC4H11NO3tris
0.5 mMC9H15O6PTCEP
0.075 %C32H58N2O8SCHAPSO

Details: CHAPSO was added only immediately prior to vitrification
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Average electron dose: 70.0 e/Å2
Details: Camera was operated in CDS mode, writing super-resolution movies with 59 frames
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5300000000000002 µm / Calibrated defocus min: 0.55 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1248538
Startup modelType of model: OTHER
Details: Initial model was generated directly from particles images using the RELION 4.0 3D initial model algorithm
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 103522
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3dw8

source_name: PDB, initial_model_type: experimental model

6e09

source_name: AlphaFold, initial_model_type: in silico model
DetailsIterating between manual refinement in Coot and automated real-space refinement in Phenix
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation
Output model

PDB-8twe:
Cryo-EM structure of the PP2A:B55-FAM122A complex, B55 body

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