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- PDB-2mse: NMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered... -

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Basic information

Entry
Database: PDB / ID: 2mse
TitleNMR data-driven model of GTPase KRas-GNP:ARafRBD complex tethered to a lipid-bilayer nanodisc
Components
  • Apolipoprotein A-I
  • GTPase KRas
  • Serine/threonine-protein kinase A-Raf
KeywordsLIPID BINDING PROTEIN / K-Ras / Nanodisc / PRE / Docking / A-RafRBD
Function / homology
Function and homology information


endocrine signaling / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption ...endocrine signaling / Defective ABCA1 causes TGD / high-density lipoprotein particle receptor binding / HDL clearance / spherical high-density lipoprotein particle / Scavenging by Class B Receptors / positive regulation of hydrolase activity / negative regulation of response to cytokine stimulus / protein oxidation / regulation of intestinal cholesterol absorption / vitamin transport / cholesterol import / blood vessel endothelial cell migration / high-density lipoprotein particle binding / negative regulation of heterotypic cell-cell adhesion / ABC transporters in lipid homeostasis / apolipoprotein A-I receptor binding / apolipoprotein receptor binding / negative regulation of cytokine production involved in immune response / negative regulation of cell adhesion molecule production / regulation of proteasomal ubiquitin-dependent protein catabolic process / HDL assembly / negative regulation of very-low-density lipoprotein particle remodeling / peptidyl-methionine modification / phosphatidylcholine biosynthetic process / glucocorticoid metabolic process / acylglycerol homeostasis / phosphatidylcholine-sterol O-acyltransferase activator activity / regulation of TOR signaling / positive regulation of phospholipid efflux / Chylomicron remodeling / positive regulation of cholesterol metabolic process / cellular response to lipoprotein particle stimulus / Chylomicron assembly / : / high-density lipoprotein particle clearance / chylomicron / phospholipid efflux / high-density lipoprotein particle remodeling / phospholipid homeostasis / reverse cholesterol transport / chemorepellent activity / high-density lipoprotein particle assembly / lipid storage / low-density lipoprotein particle / lipoprotein biosynthetic process / cholesterol transfer activity / cholesterol transport / high-density lipoprotein particle / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / very-low-density lipoprotein particle / regulation of Cdc42 protein signal transduction / triglyceride homeostasis / endothelial cell proliferation / HDL remodeling / cholesterol efflux / forebrain astrocyte development / Scavenging by Class A Receptors / negative regulation of interleukin-1 beta production / adrenal gland development / negative chemotaxis / cholesterol binding / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / cholesterol biosynthetic process / positive regulation of Rho protein signal transduction / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / amyloid-beta formation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / SOS-mediated signalling / endocytic vesicle / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / MAP kinase kinase kinase activity / positive regulation of cholesterol efflux / SHC1 events in ERBB4 signaling / negative regulation of tumor necrosis factor-mediated signaling pathway / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / Scavenging of heme from plasma / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by CSF3 (G-CSF)
Similarity search - Function
Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / small GTPase Rab1 family profile. / small GTPase Rho family profile. ...Apolipoprotein A/E / : / Apolipoprotein A1/A4/E domain / Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / small GTPase Rab1 family profile. / small GTPase Rho family profile. / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-17F / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog, isoform CRA_b / GTPase KRas / Apolipoprotein A-I / Serine/threonine-protein kinase A-Raf
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMazhab-Jafari, M. / Stathopoulos, P. / Marshall, C. / Ikura, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Oncogenic and RASopathy-associated K-RAS mutations relieve membrane-dependent occlusion of the effector-binding site.
Authors: Mazhab-Jafari, M.T. / Marshall, C.B. / Smith, M.J. / Gasmi-Seabrook, G.M. / Stathopulos, P.B. / Inagaki, F. / Kay, L.E. / Neel, B.G. / Ikura, M.
History
DepositionJul 29, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Dec 11, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref.db_code / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_db_isoform / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.details / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.3May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Apolipoprotein A-I
C: Apolipoprotein A-I
B: GTPase KRas
D: Serine/threonine-protein kinase A-Raf
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,39386
Polymers75,8624
Non-polymers63,53182
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 3000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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Protein , 3 types, 4 molecules ACBD

#1: Protein Apolipoprotein A-I / ApoA-I / Apolipoprotein A1


Mass: 23234.295 Da / Num. of mol.: 2 / Fragment: UNP residues 68-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APOA1 / Plasmid: pGBHPS MSP / Production host: Escherichia coli (E. coli) / References: UniProt: P02647
#2: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21260.250 Da / Num. of mol.: 1 / Fragment: UNP residues 1-185
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116, UniProt: A0A024RAV5*PLUS
#3: Protein Serine/threonine-protein kinase A-Raf / Proto-oncogene A-Raf / Proto-oncogene A-Raf-1 / Proto-oncogene Pks


Mass: 8133.491 Da / Num. of mol.: 1 / Fragment: UNP residues 19-91
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARAF, ARAF1, PKS, PKS2 / Plasmid: pGEX-4TpGEX-4T22 / Production host: Escherichia coli (E. coli)
References: UniProt: P10398, non-specific serine/threonine protein kinase

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Non-polymers , 4 types, 82 molecules

#4: Chemical...
ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#5: Chemical
ChemComp-17F / O-[(S)-({(2R)-2,3-bis[(9Z)-octadec-9-enoyloxy]propyl}oxy)(hydroxy)phosphoryl]-L-serine / 1,2-Dioleoyl-sn-glycero-3-phospho-L-serine


Mass: 788.043 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C42H78NO10P / Comment: phospholipid*YM
#6: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: This is a hybrid model generated by Haddock docking simulation that is based on i) NMR data that includes PRE-measurements between lipids (i.e. nanodisc) and the protien (i.e. K-RasGNP and A- ...Details: This is a hybrid model generated by Haddock docking simulation that is based on i) NMR data that includes PRE-measurements between lipids (i.e. nanodisc) and the protien (i.e. K-RasGNP and A-RafRBD) ii) crystolagraphic information (K-RasGNP and A-RafRBD) and iii) theoretical computation (i.e. nanodisc).
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HMQC
1222D 1H-13C HMQC
1332D 1H-13C HMQC
1442D 1H-13C HMQC
NMR detailsText: All PRE measurements were carrried out on the C-delta of Ile residues.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM U-15N, Ile C-delta-13C K-Ras-1, 0.6 mM membrane scaffold protein-2, 0.7 mM A-RafRBD-3, 100 mM sodium chloride-4, 5 mM Magnesium-5, 20 mM TRIS-6, 2 mM TCEP-7, 0.6 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-8, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-9, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-10, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-11, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM K-Ras-12, 0.7 mM membrane scaffold protein-13, 0.6 mM U-15N, Ile C-delta-13C A-RafRBD-14, 5 mM Magnesium-15, 20 mM TRIS-16, 100 mM sodium chloride-17, 2 mM TCEP-18, 0.7 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-19, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-20, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-21, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-22, 90% H2O/10% D2O90% H2O/10% D2O
30.6 mM U-15N, Ile C-delta-13C K-Ras-23, 0.7 mM A-RafRBD-24, 0.6 mM membrane scaffold protein-25, 20 mM TRIS-26, 100 mM sodium chloride-27, 5 mM Magnesium-28, 2 mM TCEP-29, 0.6 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-30, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-31, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-32, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-33, 0.65 mM 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)-34, 90% H2O/10% D2O90% H2O/10% D2O
40.7 mM K-Ras-35, 0.6 mM U-15N, Ile C-delta-13C A-RafRBD-36, 0.7 mM membrane scaffold protein-37, 20 mM TRIS-38, 100 mM sodium chloride-39, 5 mM Magnesium-40, 2 mM TCEP-41, 0.7 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-42, 18.75 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine-43, 5 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine-44, 1.25 mM 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-45, 0.65 mM 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)-46, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMK-Ras-1U-15N, Ile C-delta-13C1
0.6 mMmembrane scaffold protein-21
0.7 mMA-RafRBD-31
100 mMsodium chloride-41
5 mMMagnesium-51
20 mMTRIS-61
2 mMTCEP-71
0.6 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-81
18.75 mM1,2-dioleoyl-sn-glycero-3-phosphocholine-91
5 mM1,2-dioleoyl-sn-glycero-3-phospho-L-serine-101
1.25 mM1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-111
0.7 mMK-Ras-122
0.7 mMmembrane scaffold protein-132
0.6 mMA-RafRBD-14U-15N, Ile C-delta-13C2
5 mMMagnesium-152
20 mMTRIS-162
100 mMsodium chloride-172
2 mMTCEP-182
0.7 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-192
18.75 mM1,2-dioleoyl-sn-glycero-3-phosphocholine-202
5 mM1,2-dioleoyl-sn-glycero-3-phospho-L-serine-212
1.25 mM1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-222
0.6 mMK-Ras-23U-15N, Ile C-delta-13C3
0.7 mMA-RafRBD-243
0.6 mMmembrane scaffold protein-253
20 mMTRIS-263
100 mMsodium chloride-273
5 mMMagnesium-283
2 mMTCEP-293
0.6 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-303
18.75 mM1,2-dioleoyl-sn-glycero-3-phosphocholine-313
5 mM1,2-dioleoyl-sn-glycero-3-phospho-L-serine-323
1.25 mM1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-333
0.65 mM1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)-343
0.7 mMK-Ras-354
0.6 mMA-RafRBD-36U-15N, Ile C-delta-13C4
0.7 mMmembrane scaffold protein-374
20 mMTRIS-384
100 mMsodium chloride-394
5 mMMagnesium-404
2 mMTCEP-414
0.7 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-424
18.75 mM1,2-dioleoyl-sn-glycero-3-phosphocholine-434
5 mM1,2-dioleoyl-sn-glycero-3-phospho-L-serine-444
1.25 mM1,2-dioleoyl-sn-glycero-3-phosphoethanolamine-N-[4-(p-maleimidomethyl)cyclohexane-carboxamide]-454
0.65 mM1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-diethylenetriaminepentaacetic acid (gadolinium salt)-464
Sample conditionsIonic strength: 0.105 / pH: 7.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
TopSpinBruker Biospincollection
CHARMM-GUICHARMM-GUI (S. Jo, T. Kim, V.G. Iyer, and W. Im)structure solution
HADDOCKAlexandre Bonvinstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 3000 / Conformers submitted total number: 10

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