[English] 日本語
Yorodumi
- PDB-9h30: VHL:ElonginC:ElonginB-PROTAC4 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9h30
TitleVHL:ElonginC:ElonginB-PROTAC4 complex
Components
  • Elongin-B
  • Elongin-C
  • von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / PROTEIN COMPLEX / UBIQUITIN LIGASE / PROTAC / TUBULIN DEGRADATION
Function / homology
Function and homology information


regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex ...regulation of cellular response to hypoxia / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / Replication of the SARS-CoV-1 genome / VCB complex / Cul5-RING ubiquitin ligase complex / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SUMOylation of ubiquitinylation proteins / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / negative regulation of transcription elongation by RNA polymerase II / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / negative regulation of signal transduction / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / ubiquitin-like ligase-substrate adaptor activity / Formation of HIV elongation complex in the absence of HIV Tat / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / RNA Polymerase II Pre-transcription Events / negative regulation of autophagy / protein serine/threonine kinase binding / transcription corepressor binding / TP53 Regulates Transcription of DNA Repair Genes / transcription initiation at RNA polymerase II promoter / positive regulation of cell differentiation / transcription elongation by RNA polymerase II / Vif-mediated degradation of APOBEC3G / Inactivation of CSF3 (G-CSF) signaling / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / Regulation of expression of SLITs and ROBOs / cell morphogenesis / ubiquitin-protein transferase activity / transcription corepressor activity / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Neddylation / microtubule cytoskeleton / regulation of gene expression / protein-containing complex assembly / Replication of the SARS-CoV-2 genome / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / cellular response to hypoxia / molecular adaptor activity / DNA-binding transcription factor binding / amyloid fibril formation / proteasome-mediated ubiquitin-dependent protein catabolic process / protein stabilization / protein ubiquitination / cilium / negative regulation of cell population proliferation / negative regulation of gene expression / ubiquitin protein ligase binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / enzyme binding / endoplasmic reticulum / negative regulation of transcription by RNA polymerase II / mitochondrion / proteolysis / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B ...von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Elongin-C / Elongin B / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / SKP1/BTB/POZ domain superfamily / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
: / von Hippel-Lindau disease tumor suppressor / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMaiocchi, A. / Abel, A.-C. / Steinmetz, M.O. / Passarella, D. / Prota, A.E.
Funding supportEuropean Union, Switzerland, 2items
OrganizationGrant numberCountry
European Union (EU)860070 TubInTrainEuropean Union
Swiss National Science Foundation31003A_166608 Switzerland
Citation
Journal: To Be Published
Title: Effective tubulin degradation by rationally designed Proteolysis Targeting Chimeras
Authors: Maiocchi, A. / Abel, A.-C. / Basellini, M. / Perez Pena, H. / Boiarska, Z. / Ferrandi, E. / Kozicka, Z. / Fasano, V. / Pieraccini, S. / Cappelletti, G. / Steinmetz, M.O. / Prota, A.E. / Passarella, D.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 15, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: von Hippel-Lindau disease tumor suppressor
C: Elongin-C
D: Elongin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5034
Polymers45,2263
Non-polymers1,2771
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.461, 67.043, 101.845
Angle α, β, γ (deg.)90.000, 94.058, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Protein von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 22503.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: VHL / Production host: Escherichia coli (E. coli) / References: UniProt: P40337
#2: Protein Elongin-C / EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / ...EloC / Elongin 15 kDa subunit / RNA polymerase II transcription factor SIII subunit C / SIII p15 / Transcription elongation factor B polypeptide 1


Mass: 10974.616 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOC, TCEB1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15369
#3: Protein Elongin-B / EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / ...EloB / Elongin 18 kDa subunit / RNA polymerase II transcription factor SIII subunit B / SIII p18 / Transcription elongation factor B polypeptide 2


Mass: 11748.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ELOB, TCEB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15370
#4: Chemical ChemComp-A1ISE / N-[5-(1-{2-[4-({[(1S,2R,3S,5S,6S,16E,18E,20R,21S)-11-chloro-21-hydroxy-12,20-dimethoxy-2,5,9,16-tetramethyl-8,23-dioxo-4,24-dioxa-9,22-diazatetracyclo[19.3.1.1~10,14~.0~3,5~]hexacosa-10(26),11,13,16,18-pentaen-6-yl]oxy}carbonyl)phenyl]ethyl}-1H-1,2,3-triazol-4-yl)pentanoyl]-3-methyl-D-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide


Mass: 1276.928 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C66H82ClN9O13S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.7
Details: 9-11% PEG 8000, 0.2 M magnesium acetate and 0.1 M sodium cacodylate, pH 5.7

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.5→46.78 Å / Num. obs: 15196 / % possible obs: 93.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 61.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.08041 / Rpim(I) all: 0.03358 / Rrim(I) all: 0.0873 / Net I/σ(I): 10.3
Reflection shellResolution: 2.5→2.69 Å / Rmerge(I) obs: 1.147 / Mean I/σ(I) obs: 1.37 / Num. unique obs: 2987 / CC1/2: 0.771 / Rpim(I) all: 0.4627 / Rrim(I) all: 1.238

-
Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→46.78 Å / SU ML: 0.4172 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.1287
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25 713 4.95 %
Rwork0.2017 13696 -
obs0.2041 14409 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 90.84 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2686 0 90 25 2801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00252876
X-RAY DIFFRACTIONf_angle_d0.60083923
X-RAY DIFFRACTIONf_chiral_restr0.0574439
X-RAY DIFFRACTIONf_plane_restr0.0046506
X-RAY DIFFRACTIONf_dihedral_angle_d12.48351078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.690.41691010.35872075X-RAY DIFFRACTION71.79
2.69-2.960.30991520.26152892X-RAY DIFFRACTION99.09
2.96-3.390.33711520.26652880X-RAY DIFFRACTION99.28
3.39-4.270.2241530.19462906X-RAY DIFFRACTION99.35
4.28-46.780.21121550.15892943X-RAY DIFFRACTION99.14
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)
15.99496813445-0.440561813441-0.6307538733343.814757219890.2385586731983.51072643056-0.4209783975370.298451192104-0.709262247701-0.192613769551-0.02402322809760.7325497361110.120699218104-1.179643834320.3011069138850.2944412443170.09281093506520.08665976018560.427171502316-0.1303358620460.571331969323-24.223769396432.172341227810.7191880406
20.5720623077960.407468012104-0.5240025703922.000980165640.7460983633461.217692112640.0495351485532-0.01409253271830.506433165710.2878451263640.04876604653350.240307302997-0.232097384339-0.2904652198210.08647048378650.4116443763450.4038081791030.008966493037220.450792514462-0.1324263012250.703392828583-22.182901629441.490146771814.6280395471
31.46548047429-0.8723403587312.574588524454.67037164750.8592560199635.90517106616-0.325366116588-0.185410429879-0.612289964410.2188840114780.04492942728570.358038414020.712750661948-0.549016084110.262979189780.3828031551140.02967457384070.1271909046560.411288363468-0.1491865147780.696286035003-22.523053835630.457782846112.7596220858
45.02949023923-2.54825382493-0.366757056024.922810353061.380373898816.36047110918-0.21635769021-0.781724114198-0.05753123573180.1580182202970.2758030534350.4975639043790.34990331343-0.1806714114930.2486252892390.5062875601080.2242361434780.2647260295260.2667191182240.02583353714880.642965003115-20.989915119429.998481055217.4463830002
53.396317464960.183987851388-1.876498130382.02480536747-0.0004192540535682.73927949259-0.355568098958-0.9345587704120.3601781612150.3786673784890.7557945829780.44826846794-0.346293138003-0.605844426946-0.2091104177780.6331884948810.2826568070180.3223989884460.6444282941680.02517959389640.570165965648-21.065010442433.734469148323.4969651701
68.11330306545-1.79890961104-2.362878059134.960472121111.176180552511.708128913390.2245316818390.627772687901-0.00443189708706-0.921617517518-0.343647424639-0.7145491899780.3259481526320.850122273843-0.3593057356860.7068659227580.3022103064380.2223877094420.670417949969-0.002196656723050.6172983541285.369445060324.42112990718.70806505984
72.126798162983.107793559130.07580699999034.77565735509-0.7020923158132.74708782911-0.2733439781470.432656538361-2.391561404840.495514187256-0.1586700777980.02986426247651.166871389340.2328256928240.2817932449981.166653940250.434183823378-0.009094567328160.487872689255-0.1886743184951.02574275422-13.600092818520.27012920969.00305171636
87.494848627021.45512014431.699459614577.14703291842-0.2465462413562.67008540209-0.409166125228-0.922800534342-0.6445440505731.204785737860.327963952154-1.09232648786-0.264043618101-0.2335683663170.04138289984530.7625665071380.385327541702-0.116820723940.7695304653580.01558915186840.6786556048168.6554678780415.804146877834.6101205495
93.89812672786-2.29670431062.665758314477.52006401667-1.130198959532.3865743164-0.364441506731-0.605159118613-0.09339754112080.7311658345550.420778573934-0.226230571082-0.1128838958670.2314349874230.08800827739220.4046166153220.236524507587-0.0136551158860.486315809157-0.1040160519690.4329042504854.1282223246325.170745100525.2148825832
105.225345378121.42707101665-0.8472068872142.89428911386-2.732061381536.83051600166-0.156645686704-0.343763960017-0.1362245541231.19849357879-0.257713067265-0.784594848581-0.666800561568-0.8653087974770.3696572631771.270159667290.420222832897-0.4620933583231.11516786628-0.1540018922810.7825181261858.2574769406631.528199220339.6377398329
111.273023050052.10465710546-1.373578135293.479985994-2.246581334061.87500162780.0544979637955-2.034472101380.8368272732560.205600737140.5460921198240.0882822447869-1.47084490189-0.178339664147-0.8268263111261.27231010160.474243182855-0.2121235002691.1126659257-0.394473486640.8003277013047.4452209274330.764133426542.1919630996
128.05153772129-3.28720601553-6.827604923089.647060826196.112518989947.12115425248-0.520745083536-1.78479923963-0.2965802964581.76709619514-0.4524122453360.4849453631350.4058577306630.3350840655940.3997812728811.344676205960.626760999475-0.3122272994541.30155388921-0.2839303496770.7892840874418.2175878321528.395221299150.7320210879
131.322237750050.8526169017791.365597658274.278035484675.118544459727.38999354641-0.0185314120426-0.9761152420670.6971739387441.24124919271-0.918322287793-0.8865022117761.39203892511.420552692740.1481611486621.281639131860.612515682451-0.4895240127291.53644265433-0.3464162074161.5375679308516.134130178230.155102892951.6969435983
142.566270695862.528823518282.981400954822.525983347992.987731673183.53617000928-0.6344185482150.1357191303240.0937080255497-0.3058837932080.3816972190880.561908889811-2.0061827088-0.8872375362981.087097949971.477982851670.249162596242-0.3226890065511.07191914885-0.1849670681870.97459701091913.219802993341.815681567147.3095100404
153.25334043462-0.567713962262-1.012016379811.349432017962.276408604053.95182559467-0.385715733525-0.3877806579450.5439903889870.6286858486330.251867795247-0.667145920792-0.8558969838480.0280678074971-0.0367587519391.170891907190.271549130549-0.3197273529530.652908018778-0.1047714262141.0090370583813.996877139334.276618936.3258774912
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 61 through 98 )BA61 - 981 - 38
22chain 'B' and (resid 99 through 112 )BA99 - 11239 - 52
33chain 'B' and (resid 113 through 121 )BA113 - 12153 - 61
44chain 'B' and (resid 122 through 141 )BA122 - 14162 - 81
55chain 'B' and (resid 142 through 157 )BA142 - 15782 - 97
66chain 'B' and (resid 158 through 189 )BA158 - 18998 - 129
77chain 'B' and (resid 190 through 204 )BA190 - 204130 - 144
88chain 'C' and (resid 17 through 61 )CC17 - 611 - 37
99chain 'C' and (resid 62 through 112 )CC62 - 11238 - 88
1010chain 'D' and (resid 2 through 9 )DD2 - 91 - 8
1111chain 'D' and (resid 10 through 23 )DD10 - 239 - 22
1212chain 'D' and (resid 24 through 35 )DD24 - 3523 - 34
1313chain 'D' and (resid 36 through 45 )DD36 - 4535 - 44
1414chain 'D' and (resid 46 through 55 )DD46 - 5545 - 54
1515chain 'D' and (resid 56 through 103 )DD56 - 10355 - 102

+
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