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- PDB-4i5n: Structural mechanism of trimeric PP2A holoenzyme involving PR70: ... -

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Basic information

Entry
Database: PDB / ID: 4i5n
TitleStructural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation
Components
  • (Serine/threonine-protein phosphatase 2A ...) x 3
  • Microcystin-LR (MCLR) bound form
KeywordsHYDROLASE/TOXIN / EF Hand / Phosphatase / CDC6 (Substrate) / TRANSFERASE-TOXIN complex / HYDROLASE-TOXIN complex
Function / homology
Function and homology information


cellular response to vasopressin / positive regulation of chromosome segregation / CDC6 association with the ORC:origin complex / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation ...cellular response to vasopressin / positive regulation of chromosome segregation / CDC6 association with the ORC:origin complex / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / regulation of meiotic cell cycle process involved in oocyte maturation / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / positive regulation of microtubule binding / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein antigen binding / protein phosphatase regulator activity / GABA receptor binding / traversing start control point of mitotic cell cycle / DNA replication checkpoint signaling / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Initiation of Nuclear Envelope (NE) Reformation / ERKs are inactivated / Transcription of E2F targets under negative control by DREAM complex / 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 / negative regulation of epithelial to mesenchymal transition / mitotic DNA replication checkpoint signaling / cellular response to angiotensin / regulation of mitotic metaphase/anaphase transition / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / myosin phosphatase activity / intercellular bridge / regulation of cyclin-dependent protein serine/threonine kinase activity / CTLA4 inhibitory signaling / protein serine/threonine phosphatase activity / Platelet sensitization by LDL / G1/S-Specific Transcription / negative regulation of DNA replication / protein-serine/threonine phosphatase / regulation of cell differentiation / ERK/MAPK targets / positive regulation of cytokinesis / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / DNA replication origin binding / mesoderm development / phosphoprotein phosphatase activity / chromosome, centromeric region / DARPP-32 events / lateral plasma membrane / Activation of the pre-replicative complex / DNA replication initiation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / spindle midzone / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Activation of ATR in response to replication stress / Cyclin A/B1/B2 associated events during G2/M transition / 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 / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / protein dephosphorylation / meiotic cell cycle / protein tyrosine phosphatase activity / chromosome segregation / Assembly of the pre-replicative complex / RHO GTPases Activate Formins / response to lead ion / Spry regulation of FGF signaling / RAF activation / regulation of protein phosphorylation / Degradation of beta-catenin by the destruction complex / PKR-mediated signaling / tau protein binding / positive regulation of protein serine/threonine kinase activity / mitotic spindle / CDK-mediated phosphorylation and removal of Cdc6 / kinase binding / spindle pole / Orc1 removal from chromatin
Similarity search - Function
Recoverin; domain 1 - #230 / Recoverin; domain 1 - #220 / PP2A regulatory subunit B'', EF-hand domain / : / EF-hand domain / P2R3B, EF-hand / Cell division protein Cdc6/18 / Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain ...Recoverin; domain 1 - #230 / Recoverin; domain 1 - #220 / PP2A regulatory subunit B'', EF-hand domain / : / EF-hand domain / P2R3B, EF-hand / Cell division protein Cdc6/18 / Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain / : / AAA domain / AAA lid domain / AAA lid domain / HEAT repeat / 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 / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Metallo-dependent phosphatase-like / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / 4-Layer Sandwich / Armadillo-like helical / Alpha Horseshoe / EF-hand domain pair / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Microcystin-LR (MCLR) bound form / : / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Cell division control protein 6 homolog / Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
Microcystis aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsWlodarchak, N. / Satyshur, K.A. / Guo, F. / Xing, Y.
CitationJournal: Cell Res. / Year: 2013
Title: Structure of the Ca(2+)-dependent PP2A heterotrimer and insights into Cdc6 dephosphorylation.
Authors: Wlodarchak, N. / Guo, F. / Satyshur, K.A. / Jiang, L. / Jeffrey, P.D. / Sun, T. / Stanevich, V. / Mumby, M.C. / Xing, Y.
History
DepositionNov 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Structure summary
Revision 1.2Jul 24, 2013Group: Database references
Revision 1.3Aug 9, 2017Group: Advisory / Data collection ...Advisory / Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen ...diffrn_detector / entity_src_gen / pdbx_validate_polymer_linkage / software
Item: _diffrn_detector.detector
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
B: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha
D: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
E: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct
F: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha
G: Microcystin-LR (MCLR) bound form
H: Microcystin-LR (MCLR) bound form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,39916
Polymers300,0188
Non-polymers3808
Water3,117173
1
A: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
B: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct
C: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha
G: Microcystin-LR (MCLR) bound form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1998
Polymers150,0094
Non-polymers1904
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
E: Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct
F: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha
H: Microcystin-LR (MCLR) bound form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,1998
Polymers150,0094
Non-polymers1904
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.100, 101.077, 347.164
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Serine/threonine-protein phosphatase 2A ... , 3 types, 6 molecules ADBECF

#1: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Medium tumor antigen-associated 61 kDa protein / PP2A subunit A isoform PR65-alpha / PP2A subunit A ...Medium tumor antigen-associated 61 kDa protein / PP2A subunit A isoform PR65-alpha / PP2A subunit A isoform R1-alpha


Mass: 65563.461 Da / Num. of mol.: 2 / Fragment: PP2A A alpha subunit (9-589)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Plasmid: pCool / Cell line (production host): DH5a / Production host: Escherichia coli (E. coli) / References: UniProt: P30153
#2: Protein Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct / PP2A subunit B isoform PR48 Protein phosphatase 2A 48 kDa regulatory subunit


Mass: 47649.289 Da / Num. of mol.: 2
Fragment: UNP Q9Y5P8 residues 122-490 and UNP Q99741 residues 70-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R3B, PPP2R3L / Plasmid: PQlinkG / Cell line (production host): DH5a / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5P8, UniProt: Q99741
#3: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha


Mass: 35780.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Plasmid: FBQH / Cell line (production host): high5 / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: P67775, protein-serine/threonine phosphatase

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Protein/peptide , 1 types, 2 molecules GH

#4: Protein/peptide Microcystin-LR (MCLR) bound form


Type: Oligopeptide / Class: Toxin / Mass: 1016.211 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Microcystis aeruginosa (bacteria) / References: Microcystin-LR (MCLR) bound form

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Non-polymers , 3 types, 181 molecules

#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE LINKER IS DERIVED FROM JMJD6

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.75
Details: 0.03M Succinic acid with 7% PEG 3350. Protein (6.2mg/mL) in 10mM tris pH 8.0, 150mM NaCl, 5mM DTT, 1mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97987 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97987 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 119018 / Num. obs: 119018 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rsym value: 0.157 / Net I/σ(I): 11.85
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 4.8 % / % possible all: 99

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CRANKphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→49.08 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.541 / SU ML: 0.261 / Cross valid method: THROUGHOUT / ESU R Free: 0.356 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24963 4113 4.9 %RANDOM
Rwork0.18315 ---
obs0.18642 79333 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.432 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å2-0 Å2-0 Å2
2---0.78 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.8→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19745 0 8 173 19926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01920202
X-RAY DIFFRACTIONr_bond_other_d0.0020.0219253
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.97427309
X-RAY DIFFRACTIONr_angle_other_deg1.1513.00144296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.22252465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.59924.136943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.196153377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.23715133
X-RAY DIFFRACTIONr_chiral_restr0.0790.23087
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02122650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024607
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 296 -
Rwork0.283 5786 -
obs--100 %

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