[English] 日本語
Yorodumi
- PDB-6u09: Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6u09
TitleDiscovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking
ComponentsEukaryotic translation initiation factor 4EEIF4E
KeywordsTRANSLATION/INHIBITOR / cap-binding site / anti-neoplastic / inhibitor / translation initiation blocking / TRANSLATION-INHIBITOR complex
Function / homology
Function and homology information


Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / Transport of Mature mRNA Derived from an Intronless Transcript / Deadenylation of mRNA / Translation initiation complex formation / Ribosomal scanning and start codon recognition / ISG15 antiviral mechanism / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / mTORC1-mediated signalling / : / eukaryotic initiation factor 4G binding / regulation of translation at postsynapse, modulating synaptic transmission / chromatoid body / eukaryotic translation initiation factor 4F complex / mRNA cap binding / RNA 7-methylguanosine cap binding / nuclear export / RISC complex / postsynaptic cytosol / stem cell population maintenance / negative regulation of neuron differentiation / behavioral fear response / mRNA export from nucleus / translational initiation / translation initiation factor activity / positive regulation of mitotic cell cycle / cellular response to dexamethasone stimulus / P-body / neuron differentiation / G1/S transition of mitotic cell cycle / cytoplasmic stress granule / cytoplasmic ribonucleoprotein granule / regulation of translation / postsynapse / DNA-binding transcription factor binding / negative regulation of translation / nuclear body / nuclear speck / translation / glutamatergic synapse / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
RNA Cap, Translation Initiation Factor Eif4e / RNA Cap, Translation Initiation Factor Eif4e / Eukaryotic translation initiation factor 4E (eIF-4E), conserved site / Eukaryotic initiation factor 4E signature. / Translation Initiation factor eIF- 4e / Eukaryotic initiation factor 4E / Translation Initiation factor eIF- 4e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EI9 / Eukaryotic translation initiation factor 4E
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWan, X.B. / Shoichet, B.K. / Taunton, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R35 GM122481 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Discovery of Lysine-Targeted eIF4E Inhibitors through Covalent Docking.
Authors: Wan, X. / Yang, T. / Cuesta, A. / Pang, X. / Balius, T.E. / Irwin, J.J. / Shoichet, B.K. / Taunton, J.
History
DepositionAug 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eukaryotic translation initiation factor 4E
B: Eukaryotic translation initiation factor 4E
C: Eukaryotic translation initiation factor 4E
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,4748
Polymers88,5804
Non-polymers1,8944
Water4,378243
1
A: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6192
Polymers22,1451
Non-polymers4731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6192
Polymers22,1451
Non-polymers4731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6192
Polymers22,1451
Non-polymers4731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 4E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6192
Polymers22,1451
Non-polymers4731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.100, 38.240, 147.790
Angle α, β, γ (deg.)95.500, 87.280, 101.850
Int Tables number1
Space group name H-MP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
Eukaryotic translation initiation factor 4E / EIF4E / mRNA cap-binding protein / eIF-4F 25 kDa subunit


Mass: 22145.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: covalent lysine inhibitor / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Eif4e / Production host: Escherichia coli (E. coli) / References: UniProt: P63073
#2: Chemical
ChemComp-EI9 / 3-{(1-oxo-1,2-dihydroisoquinolin-7-yl)[(pyridin-4-yl)methyl]sulfamoyl}benzene-1-sulfonyl fluoride


Mass: 473.497 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H16FN3O5S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.2 / Details: HEPES, MPD, PEG 6K, NDSB-256

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12011 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12011 Å / Relative weight: 1
ReflectionResolution: 1.13→146.99 Å / Num. obs: 202752 / % possible obs: 66.2 % / Redundancy: 3.3 % / Biso Wilson estimate: 28.59 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.044 / Rrim(I) all: 0.082 / Net I/σ(I): 5.3 / Num. measured all: 674897 / Scaling rejects: 13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allNet I/σ(I) obs% possible allCC1/2
1.13-1.151.72.2932701581.9813.0470.41
6.17-146.993.80.027682718160.0160.03132.897.40.999

-
Processing

Software
NameVersionClassification
PHENIXphenix-1.13-2998refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DT6

4dt6


Resolution: 1.79→73.525 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2383 3466 4.83 %
Rwork0.1908 68306 -
obs0.193 71772 93.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.01 Å2 / Biso mean: 43.6788 Å2 / Biso min: 15.69 Å2
Refinement stepCycle: final / Resolution: 1.79→73.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5896 0 124 243 6263
Biso mean--79.58 41.74 -
Num. residues----730
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.79-1.81460.3871310.3269273991
1.8146-1.84050.35921120.3149262591
1.8405-1.8680.34191440.3036261991
1.868-1.89710.33161310.2784276092
1.8971-1.92820.28261400.2758265192
1.9282-1.96150.30271430.2561262592
1.9615-1.99720.25631510.2407276993
1.9972-2.03560.30731610.2307262393
2.0356-2.07710.25311140.217269192
2.0771-2.12230.25141100.216285494
2.1223-2.17170.2571490.2091263793
2.1717-2.2260.2621300.21277894
2.226-2.28620.23021310.1978274094
2.2862-2.35350.24421450.1945269794
2.3535-2.42940.23651520.1925274895
2.4294-2.51630.25771720.1982273094
2.5163-2.6170.27751390.1948272195
2.617-2.73610.24831650.1895278895
2.7361-2.88040.24881170.1954277295
2.8804-3.06080.25091180.1828275895
3.0608-3.29720.22861370.1807279095
3.2972-3.6290.20971280.1734277495
3.629-4.15410.21211560.1592280596
4.1541-5.23350.1941410.1592277396
5.2335-73.5250.22711490.1812283997
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)
15.06710.6992-2.89525.35860.33642.8957-0.1680.1108-0.3446-0.35740.2635-0.67120.07370.7708-0.10530.32270.0873-0.01710.3752-0.10610.418724.5491-11.82627.3469
29.9529-1.3575-1.3020.61360.41430.6321-0.07950.3886-0.2459-0.0264-0.1280.38180.0518-0.44150.17260.2571-0.0021-0.01210.3276-0.06280.4325-3.8139-2.89315.039
37.701-0.4524-4.27710.06810.19662.61720.07240.51020.11240.0256-0.24370.5583-0.2958-0.67030.23360.2618-0.041-0.03370.2528-0.1360.54621.1537-6.985212.0786
42.7375-0.6995-0.93482.7050.30243.1442-0.02390.1708-0.1545-0.1525-0.01730.262-0.1462-0.17520.02660.2002-0.0199-0.03050.1627-0.02470.24688.64930.479310.4727
56.78690.6974-2.03223.55750.56782.264-0.0637-0.0713-0.51680.5930.01110.28950.5426-0.68250.04210.38240.01440.07660.24660.03280.30312.6443-10.914725.8141
61.7089-0.1894-0.50322.5913-0.09763.0777-0.0204-0.22420.06180.32780.0439-0.0015-0.12440.1253-0.00730.2114-0.0033-0.01020.1449-0.03090.21912.22173.841225.5615
70.93282.382-0.03556.17390.6124.24330.2501-0.49910.84360.8388-0.35871.1292-0.276-0.822-0.05970.41240.01380.1160.3081-0.06250.40495.17751.046335.9222
84.6655-0.93821.67495.229-3.43894.25090.4116-0.1168-0.320.1198-0.6095-0.49520.70030.3775-0.15210.2895-0.004-0.10230.36930.04220.425338.99644.464668.9868
91.3897-2.033-0.29876.4344-0.20360.503-0.00110.13810.46270.2073-0.2131-0.2212-0.3133-0.11660.23670.25980.0051-0.06270.2907-0.0050.42427.09728.400562.5589
103.0392-0.01390.29752.3097-0.76583.4112-0.0197-0.29060.03160.2151-0.01610.1042-0.269-0.190.04720.1573-0.0009-0.03140.212-0.02370.228724.176817.055766.2749
112.33841.00070.15224.4343-0.9729.2359-0.15960.13620.3971-0.0980.0726-0.2308-0.9928-0.0480.1210.2602-0.06340.01140.27420.04750.34333.876524.938550.7605
122.877-0.1511-1.78660.80520.04972.48740.02260.16650.3615-0.18430.00450.4807-0.113-0.5353-0.03670.2072-0.0405-0.03320.4155-0.0230.358412.629816.16953.5291
132.00440.13470.04472.7173-0.40793.198-0.00420.23440.0166-0.2628-0.0616-0.06130.1143-0.02560.07640.1421-0.0144-0.0150.2127-0.00220.224125.1914.195553.1952
147.6240.2778-2.7954.7504-0.40035.21260.10180.9028-0.2673-0.3838-0.09180.05590.4299-0.53360.09170.3272-0.0161-0.02680.2756-0.0920.225.13487.10345.1771
154.33322.5929-0.82053.2929-0.94673.6627-0.19060.67370.2436-0.52190.34380.26470.0998-0.172-0.18260.2781-0.0381-0.05780.3824-0.00010.302919.652215.677242.6426
163.19950.2425-0.24523.0754-0.07453.97470.316-0.6775-0.34920.2408-0.25430.0221-0.01290.4154-0.03570.20290.0645-0.04190.41520.02070.312314.17719.879681.1133
173.92843.07130.65128.12360.32480.81030.0348-0.2623-1.03910.0986-0.22310.13080.57160.44630.10670.33450.10520.03920.57830.06120.582210.4216-2.087183.5981
181.97530.2588-0.31252.017-0.77162.7335-0.0127-0.1053-0.3974-0.07180.14150.08590.2448-0.2298-0.11440.2099-0.028-0.01860.47440.05910.29455.03728.1281.0677
192.5189-0.3807-2.23015.3271-0.89012.24580.0458-0.4857-0.25090.5227-0.0418-0.12170.64930.295-0.00140.4211-0.0251-0.09130.78410.16850.386615.04390.193696.9479
205.9403-1.29194.22391.9836-1.32754.02080.1644-0.5103-0.16440.19520.07240.50750.2005-0.4491-0.29130.3441-0.02220.04460.81750.07510.4068-6.35519.052693.7887
211.878-0.1419-0.52352.8261-0.50633.16720.0981-0.7535-0.13440.363-0.00990.0447-0.4569-0.1591-0.04810.2866-0.00210.02990.59540.0390.24537.340914.165892.0456
223.1110.06510.81122.5303-0.37713.0891-0.0035-0.83670.05360.6861-0.05160.3257-0.0578-0.2020.01250.3669-0.02550.06470.70480.0420.27773.388810.5511101.8306
234.91790.2496-3.01654.3571-2.71993.8756-0.2420.122-0.2818-0.39610.28530.12150.4918-0.7926-0.1140.4536-0.0561-0.08080.3409-0.02890.24244.39653.1499-1.3727
247.73133.44150.09445.68750.07053.6736-0.06650.38940.2832-0.75330.0037-1.25040.16960.9601-0.04540.38350.07240.16580.41020.0290.59826.184222.5711-8.31
252.2120.6417-0.72633.5645-0.59852.25290.0687-0.19490.1012-0.1408-0.1031-0.2487-0.09890.20260.01660.43150.04720.01460.2053-0.00850.245514.588919.8476-4.165
265.9314-0.2981-0.53831.58430.30631.9329-0.07240.51050.2771-0.84590.1649-0.74930.3541.0318-0.09210.78120.04710.21540.4446-0.03290.474323.098412.9088-20.2626
270.79860.023-0.37121.08270.04012.03210.25890.11970.3174-0.5652-0.2768-0.0837-0.4064-0.1768-0.10140.88450.04260.04720.2510.02450.39059.933531.9026-17.0371
282.9628-0.50840.28730.89730.89813.69130.01470.3445-0.0685-1.15780.0811-0.12020.1657-0.4826-0.01260.6556-0.0422-0.010.2537-0.00440.21557.947717.6526-15.199
293.0667-0.660.1320.17320.0531.1176-0.00440.54740.472-1.3599-0.1763-0.49210.11770.3307-0.43931.13410.00050.22210.33150.05720.137915.746222.6354-21.2309
303.3410.5137-1.70631.69981.09762.20020.58050.69490.1021-1.46060.13160.7640.4041-0.90050.07320.98450.0633-0.18990.47290.06550.22883.004621.7069-24.4959
313.7547-2.56771.97883.3841-0.21961.94490.31960.59020.2187-1.0686-0.346-0.7139-0.21860.77230.03871.03550.0480.1080.58840.08830.25916.042122.7317-29.7538
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 42 )A30 - 42
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 56 )A43 - 56
3X-RAY DIFFRACTION3chain 'A' and (resid 57 through 66 )A57 - 66
4X-RAY DIFFRACTION4chain 'A' and (resid 67 through 95 )A67 - 95
5X-RAY DIFFRACTION5chain 'A' and (resid 96 through 110 )A96 - 110
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 195 )A111 - 195
7X-RAY DIFFRACTION7chain 'A' and (resid 196 through 217 )A196 - 217
8X-RAY DIFFRACTION8chain 'B' and (resid 31 through 42 )B31 - 42
9X-RAY DIFFRACTION9chain 'B' and (resid 43 through 66 )B43 - 66
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 95 )B67 - 95
11X-RAY DIFFRACTION11chain 'B' and (resid 96 through 110 )B96 - 110
12X-RAY DIFFRACTION12chain 'B' and (resid 111 through 125 )B111 - 125
13X-RAY DIFFRACTION13chain 'B' and (resid 126 through 172 )B126 - 172
14X-RAY DIFFRACTION14chain 'B' and (resid 173 through 186 )B173 - 186
15X-RAY DIFFRACTION15chain 'B' and (resid 187 through 217 )B187 - 217
16X-RAY DIFFRACTION16chain 'C' and (resid 28 through 55 )C28 - 55
17X-RAY DIFFRACTION17chain 'C' and (resid 56 through 66 )C56 - 66
18X-RAY DIFFRACTION18chain 'C' and (resid 67 through 95 )C67 - 95
19X-RAY DIFFRACTION19chain 'C' and (resid 96 through 110 )C96 - 110
20X-RAY DIFFRACTION20chain 'C' and (resid 111 through 125 )C111 - 125
21X-RAY DIFFRACTION21chain 'C' and (resid 126 through 155 )C126 - 155
22X-RAY DIFFRACTION22chain 'C' and (resid 156 through 217 )C156 - 217
23X-RAY DIFFRACTION23chain 'D' and (resid 29 through 42 )D29 - 42
24X-RAY DIFFRACTION24chain 'D' and (resid 43 through 60 )D43 - 60
25X-RAY DIFFRACTION25chain 'D' and (resid 61 through 95 )D61 - 95
26X-RAY DIFFRACTION26chain 'D' and (resid 96 through 110 )D96 - 110
27X-RAY DIFFRACTION27chain 'D' and (resid 111 through 125 )D111 - 125
28X-RAY DIFFRACTION28chain 'D' and (resid 126 through 155 )D126 - 155
29X-RAY DIFFRACTION29chain 'D' and (resid 156 through 172 )D156 - 172
30X-RAY DIFFRACTION30chain 'D' and (resid 173 through 195 )D173 - 195
31X-RAY DIFFRACTION31chain 'D' and (resid 196 through 217 )D196 - 217

+
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