[English] 日本語
Yorodumi
- PDB-6v94: Expanding the Chemical Landscape of SOS1 Activators Using Fragmen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6v94
TitleExpanding the Chemical Landscape of SOS1 Activators Using Fragment Based Methods
Components
  • (GTPase HRasHRAS) x 2
  • Son of sevenless homolog 1
KeywordsSIGNALING PROTEIN / Ras / SOS / inhibitor / ONCOPROTEIN / Protein-protein complex / MAPK
Function / homology
Function and homology information


midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / oncogene-induced cell senescence / positive regulation of ruffle assembly / blood vessel morphogenesis / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of miRNA metabolic process / T-helper 1 type immune response / Regulation of KIT signaling / epidermal growth factor receptor binding / positive regulation of wound healing / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / defense response to protozoan / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / RAS signaling downstream of NF1 loss-of-function variants / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / RET signaling / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / Signalling to RAS / fibroblast growth factor receptor signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / adipose tissue development / Signal attenuation / Estrogen-stimulated signaling through PRKCZ / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / RAC1 GTPase cycle / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / molecular condensate scaffold activity / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GTPase activator activity / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / intrinsic apoptotic signaling pathway / guanyl-nucleotide exchange factor activity / small monomeric GTPase / G protein activity / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants
Similarity search - Function
Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain ...Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Small GTPase, Ras-type / small GTPase Ras family profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Histone-fold / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FORMIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Chem-QTV / GTPase HRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsPhan, J. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Lustgarten Foundation United States
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Sulfonamide-Derived Agonists of SOS1-Mediated Nucleotide Exchange on RAS Using Fragment-Based Methods.
Authors: Sarkar, D. / Olejniczak, E.T. / Phan, J. / Coker, J.A. / Sai, J. / Arnold, A. / Beesetty, Y. / Waterson, A.G. / Fesik, S.W.
History
DepositionDec 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GTPase HRas
B: Son of sevenless homolog 1
C: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,64315
Polymers94,3783
Non-polymers1,26512
Water20,7351151
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-38 kcal/mol
Surface area35730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.832, 183.832, 178.605
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2842-

HOH

-
Components

-
Protein , 3 types, 3 molecules ABC

#1: Protein GTPase HRas / HRAS / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18856.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112
#2: Protein Son of sevenless homolog 1 / SOS-1


Mass: 56589.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07889
#3: Protein GTPase HRas / HRAS / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18932.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112

-
Non-polymers , 7 types, 1163 molecules

#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-QTV / 1-[(4-fluorophenyl)methyl]-2-methyl-4-nitro-1H-imidazole


Mass: 235.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10FN3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1151 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4 Å3/Da / Density % sol: 69.23 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 4 / Details: 0.1 M sodium acetate, 2.0 M sodium formate, pH 4.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 140282 / % possible obs: 99.9 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.03 / Rrim(I) all: 0.102 / Χ2: 0.963 / Net I/σ(I): 9 / Num. measured all: 1635867
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8310.70.87569550.8310.280.921.06399.8
1.83-1.8610.80.75969210.8650.2420.7981.07699.8
1.86-1.910.90.66669620.8940.2110.71.09899.9
1.9-1.94110.55869320.9190.1760.5861.07599.9
1.94-1.98110.47169310.9420.1480.4941.06299.9
1.98-2.0311.20.38469640.9620.120.4031.01999.9
2.03-2.0811.20.33569670.9720.1040.3511.017100
2.08-2.1311.30.27469750.9810.0850.2871.006100
2.13-2.211.50.2369460.9860.0710.2410.963100
2.2-2.2711.60.19869680.9890.0610.2070.903100
2.27-2.3511.70.1769940.9920.0520.1780.922100
2.35-2.4411.80.14769910.9930.0450.1540.864100
2.44-2.5511.90.12870150.9950.0390.1340.826100
2.55-2.6912.10.11869910.9950.0350.1230.826100
2.69-2.8612.30.10270110.9970.030.1060.795100
2.86-3.0812.50.08370530.9980.0240.0860.916100
3.08-3.3912.60.06170580.9990.0180.0630.931100
3.39-3.8812.60.04670940.9990.0130.0480.885100
3.88-4.8812.50.03571530.9990.010.0360.915100
4.88-5011.90.03474010.9990.010.0361.17899.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYI

4nyi


Resolution: 1.8→48.72 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.43
RfactorNum. reflection% reflection
Rfree0.1718 1997 1.42 %
Rwork0.1583 --
obs0.1585 140269 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.26 Å2 / Biso mean: 24.0919 Å2 / Biso min: 1.58 Å2
Refinement stepCycle: final / Resolution: 1.8→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 81 1157 7772
Biso mean--28.08 38.19 -
Num. residues----802
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.840.23931390.22089667980699
1.84-1.890.25481460.203297329878100
1.89-1.950.19061340.186398449978100
1.95-2.010.19421380.173197729910100
2.01-2.080.20251490.1798309979100
2.08-2.170.16481460.159997889934100
2.17-2.260.17421380.156798339971100
2.26-2.380.1761430.1552986110004100
2.38-2.530.15531410.1558986210003100
2.53-2.730.1811460.1644986510011100
2.73-30.18771420.1648991110053100
3-3.440.16251410.1538995810099100
3.44-4.330.13981430.1321002910172100
4.33-48.720.15971510.15281032010471100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0028-0.0085-0.04540.18780.00840.04460.07060.0128-0.0133-0.1082-0.02780.02890.03120.04320.00480.10230.01730.01590.08010.00450.111223.25948.684231.6256
20.0386-0.05110.03750.1407-0.030.06420.0926-0.010.0012-0.1088-0.03970.24190.0966-0.0010.01310.13920.00590.00670.1022-0.03070.18517.9968-1.690336.3359
30.0408-0.05220.02460.1001-0.02760.03250.0059-0.04090.00310.0046-0.0074-0.12340.098-0.04770.00460.10060.03130.01150.089-0.01180.148432.36062.39239.6181
40.05140.05690.03150.07760.03830.08820.03360.0095-0.0418-0.0011-0.00660.07120.0817-0.04860.00180.1112-0.02820.0150.1269-0.01610.122319.53750.11962.2209
50.03860.0070.0590.00550.00620.06140.0006-0.09010.01220.07450.046-0.0366-0.090.0519-00.1303-0.05370.01810.16-0.02030.114829.368845.08656.4983
60.01830.00680.0099-0.00710.00090.0140.0029-0.1273-0.17130.1594-0.08210.0640.1593-0.03350.00130.2153-0.06830.03130.19550.01230.131422.679946.013873.8798
70.07910.07860.01520.08790.01240.02540.1076-0.20340.06620.1078-0.04870.0361-0.03480.07030.00320.1414-0.04640.02030.1597-0.03220.114827.515156.434874.0817
80.0660.1014-0.06220.1089-0.08180.05910.0754-0.00680.1858-0.0329-0.05010.0915-0.10780.07410.00320.1491-0.03340.03270.1055-0.02680.169124.576865.968465.6266
90.015-0.0123-0.01390.0111-0.00450.02030.0270.03560.03710.0008-0.10020.0183-0.04510.1448-0.00010.1311-0.05360.02140.1577-0.01470.100834.497653.90960.4445
100.0585-0.1506-0.13870.10970.02720.2148-0.0086-0.01740.02280.01640.01680.006-0.00560.0909-00.1241-0.02230.00440.12860.00450.086315.427130.659680.0593
110.11350.1369-0.056-0.0612-0.06590.31510.0094-0.0070.0083-0.01030.00760.0418-0.0466-0.0601-0.01290.0792-0.00490.00920.08670.0010.08929.444240.408348.842
120.12570.042-0.09190.2896-0.10820.5475-0.0320.016-0.0031-0.02740.0253-0.01590.00860.0427-0.00870.0478-0.02140.00990.0579-0.00780.053723.952833.184732.0959
130.0029-0.01580.01280.0742-0.0410.0207-0.08110.03940.1480.11580.0376-0.13770.04470.0187-00.09780.0186-0.00690.1033-0.00180.182531.48512.091441.6274
140.07760.05660.05030.04090.03320.03460.08110.044-0.05290.05740.07290.02480.12370.01230.02940.30060.0487-0.15540.10350.08740.344632.149612.597755.7726
150.01310.009-0.01960.0023-0.00480.0098-0.0206-0.0508-0.02860.0365-0.1101-0.0552-0.11150.1347-0.00010.2130.058-0.09640.245-0.00710.41539.983214.178545.8475
160.03170.04130.05540.10950.06790.041-0.03050.0076-0.0373-0.0218-0.0121-0.16-0.0392-0.01690.00010.0832-0.00070.01070.07310.01260.15429.383518.961836.1102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 75 through 117 )C75 - 117
2X-RAY DIFFRACTION2chain 'C' and (resid 118 through 137 )C118 - 137
3X-RAY DIFFRACTION3chain 'C' and (resid 138 through 166 )C138 - 166
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 36 )A1 - 36
5X-RAY DIFFRACTION5chain 'A' and (resid 37 through 52 )A37 - 52
6X-RAY DIFFRACTION6chain 'A' and (resid 53 through 74 )A53 - 74
7X-RAY DIFFRACTION7chain 'A' and (resid 75 through 116 )A75 - 116
8X-RAY DIFFRACTION8chain 'A' and (resid 117 through 151 )A117 - 151
9X-RAY DIFFRACTION9chain 'A' and (resid 152 through 166 )A152 - 166
10X-RAY DIFFRACTION10chain 'B' and (resid 565 through 699 )B565 - 699
11X-RAY DIFFRACTION11chain 'B' and (resid 700 through 818 )B700 - 818
12X-RAY DIFFRACTION12chain 'B' and (resid 819 through 1046 )B819 - 1046
13X-RAY DIFFRACTION13chain 'C' and (resid 0 through 24 )C0 - 24
14X-RAY DIFFRACTION14chain 'C' and (resid 25 through 34 )C25 - 34
15X-RAY DIFFRACTION15chain 'C' and (resid 35 through 48 )C35 - 48
16X-RAY DIFFRACTION16chain 'C' and (resid 49 through 74 )C49 - 74

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more