[English] 日本語
Yorodumi
- PDB-5n4w: Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5n4w
TitleCrystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex
Components
  • Cullin-2
  • E3 ubiquitin-protein ligase RBX1
  • Elongin-B
  • Elongin-C
  • Von Hippel-Lindau disease tumor suppressor
KeywordsLIGASE / Cullin RING / E3 ubiquitin ligase / VHL / Cullin-2
Function / homology
Function and homology information


regulation of cellular response to hypoxia / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling ...regulation of cellular response to hypoxia / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / RHOBTB3 ATPase cycle / negative regulation of receptor signaling pathway via JAK-STAT / Cul7-RING ubiquitin ligase complex / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / transcription elongation factor activity / target-directed miRNA degradation / elongin complex / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / Replication of the SARS-CoV-1 genome / NEDD8 ligase activity / VCB complex / negative regulation of response to oxidative stress / Cul5-RING ubiquitin ligase complex / SCF ubiquitin ligase complex / negative regulation of type I interferon production / ubiquitin-ubiquitin ligase activity / Cul2-RING ubiquitin ligase complex / intracellular membraneless organelle / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Cul4-RING E3 ubiquitin ligase complex / Cul3-RING ubiquitin ligase complex / Cul4B-RING E3 ubiquitin ligase complex / ubiquitin ligase complex scaffold activity / negative regulation of mitophagy / SUMOylation of ubiquitinylation proteins / Prolactin receptor signaling / cullin family protein binding / 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 / protein monoubiquitination / 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 / protein K48-linked ubiquitination / Formation of HIV elongation complex in the absence of HIV Tat / Nuclear events stimulated by ALK signaling in cancer / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of TORC1 signaling / transcription-coupled nucleotide-excision repair / RNA Polymerase II Pre-transcription Events / positive regulation of TORC1 signaling / regulation of cellular response to insulin stimulus / intrinsic apoptotic signaling pathway / negative regulation of insulin receptor signaling pathway / post-translational protein modification / negative regulation of autophagy / protein serine/threonine kinase binding / Regulation of BACH1 activity / T cell activation / transcription corepressor binding / positive regulation of cell differentiation / Degradation of DVL / TP53 Regulates Transcription of DNA Repair Genes / cellular response to amino acid stimulus / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / Degradation of GLI1 by the proteasome / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / G1/S transition of mitotic cell cycle / negative regulation of canonical Wnt signaling pathway / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / DNA Damage Recognition in GG-NER / Inactivation of CSF3 (G-CSF) signaling / Degradation of beta-catenin by the destruction complex / RING-type E3 ubiquitin transferase / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Evasion by RSV of host interferon responses / NOTCH1 Intracellular Domain Regulates Transcription / Dual Incision in GG-NER / Transcription-Coupled Nucleotide Excision Repair (TC-NER) / Formation of TC-NER Pre-Incision Complex / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / Regulation of expression of SLITs and ROBOs / Formation of Incision Complex in GG-NER / Interleukin-1 signaling / Orc1 removal from chromatin / cell morphogenesis / protein polyubiquitination / Dual incision in TC-NER
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 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain ...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 / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin family signature. / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Elongin-C / Elongin B / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / Cullin / Cullin, N-terminal / Cullin homology domain / Cullin homology domain superfamily / Cullin alpha solenoid domain / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / SKP1/BTB/POZ domain superfamily / Zinc finger RING-type profile. / Zinc finger, RING-type / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
von Hippel-Lindau disease tumor suppressor / E3 ubiquitin-protein ligase RBX1 / Cullin-2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsCardote, T.A.F. / Gadd, M.S. / Ciulli, A.
Funding support United Kingdom, Portugal, 2items
OrganizationGrant numberCountry
European Research CouncilERC-2012-StG-311460 United Kingdom
Fundacao para a Ciencia e TecnologiaSFRH/BD/92417/2013 Portugal
CitationJournal: Structure / Year: 2017
Title: Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex.
Authors: Cardote, T.A.F. / Gadd, M.S. / Ciulli, A.
History
DepositionFeb 11, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _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_PubMed / _citation.title
Revision 1.2Oct 24, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.3Apr 24, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_cell_line
Revision 1.4May 1, 2024Group: 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: Cullin-2
V: Von Hippel-Lindau disease tumor suppressor
R: E3 ubiquitin-protein ligase RBX1
B: Elongin-B
C: Elongin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,3778
Polymers140,1815
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10350 Å2
ΔGint-174 kcal/mol
Surface area56520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.038, 190.962, 238.885
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

-
Protein , 5 types, 5 molecules AVRBC

#1: Protein Cullin-2 / CUL-2


Mass: 87300.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CUL2 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13617
#2: Protein Von Hippel-Lindau disease tumor suppressor / Protein G7 / pVHL


Mass: 18558.162 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
#3: Protein E3 ubiquitin-protein ligase RBX1 / Protein ZYP / RING finger protein 75 / RING-box protein 1 / Rbx1 / Regulator of cullins 1


Mass: 11599.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RBX1, RNF75, ROC1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P62877, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#4: 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
#5: 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

-
Non-polymers , 1 types, 3 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Zn / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 0.1 M Tris pH 7.6, 0.15 M ammonium sulphate, 15% polyethyleneglycol 4000 and 3% 1,4-dioxane or 4% acetonitrile. The sample was crystallised in the presence of a 19-mer peptide mimicking the ...Details: 0.1 M Tris pH 7.6, 0.15 M ammonium sulphate, 15% polyethyleneglycol 4000 and 3% 1,4-dioxane or 4% acetonitrile. The sample was crystallised in the presence of a 19-mer peptide mimicking the substrate HIF-1alpha - residues 559-577 (DEALAPYIPMDDDFQLRSF, with the mutations L559D and M561A and P564 is hydroxyproline).

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.928 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 3.9→95.481 Å / Num. obs: 34407 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 200 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 10.2
Reflection shellResolution: 3.9→4.27 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 2.2 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2558: ???)refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HOMOLOGY MODEL

Resolution: 3.9→95.48 Å / SU ML: 0.68 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.04
RfactorNum. reflection% reflection
Rfree0.346 1802 5.24 %
Rwork0.302 --
obs0.304 34407 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 191 Å2
Refinement stepCycle: LAST / Resolution: 3.9→95.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7716 0 3 0 7719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037855
X-RAY DIFFRACTIONf_angle_d0.69210574
X-RAY DIFFRACTIONf_dihedral_angle_d3.4995127
X-RAY DIFFRACTIONf_chiral_restr0.0431195
X-RAY DIFFRACTIONf_plane_restr0.0041346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9001-4.00550.40261350.39732482X-RAY DIFFRACTION99
4.0055-4.12340.37711330.35062509X-RAY DIFFRACTION99
4.1234-4.25650.39821350.3412448X-RAY DIFFRACTION98
4.2565-4.40860.36071420.32152506X-RAY DIFFRACTION100
4.4086-4.58510.34381340.31032568X-RAY DIFFRACTION100
4.5851-4.79380.31491590.30682493X-RAY DIFFRACTION99
4.7938-5.04650.37581620.29742485X-RAY DIFFRACTION100
5.0465-5.36270.32051290.30192513X-RAY DIFFRACTION99
5.3627-5.77670.38841260.33892555X-RAY DIFFRACTION99
5.7767-6.35790.38231390.36542479X-RAY DIFFRACTION99
6.3579-7.27760.39681320.34632534X-RAY DIFFRACTION100
7.2776-9.16780.41641440.29652510X-RAY DIFFRACTION100
9.1678-95.50960.25431320.23782523X-RAY DIFFRACTION99
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)
10.4416-0.9161-0.47042.60240.03270.98591.411-0.8893-0.4805-0.5002-0.44730.04070.58730.24980.78961.0689-0.3334-0.68352.22870.08691.4286-22.33453.0801-61.2783
22.66011.59571.56721.8008-0.72094.46240.51510.497-1.581-0.3201-0.4902-0.62681.9262-0.138-1.90910.8643-0.2563-0.14991.2219-0.44840.38611.7137-6.9799-34.8271
36.60252.29553.06744.31823.57454.01870.58960.07041.01210.5913-0.6006-0.59311.1456-0.2406-0.18751.0145-0.1987-0.04580.69230.21880.697828.4753.989-10.4271
43.38872.36561.20592.7737-0.6651.14650.4383-0.4654-0.52720.7327-0.1995-0.2278-0.42480.0227-0.20871.2817-0.027-0.13240.9750.01451.273944.504934.32778.3282
53.8191.39461.620.65871.09742.3176-0.08450.07870.28-0.5578-0.07920.4548-0.25680.25310.26072.75992.2711-0.04164.91350.58931.7178-27.416636.3384-64.3799
60.2834-0.0082-0.67990.0010.01441.6384-0.3704-0.04630.13890.2860.0839-0.05990.5034-0.04160.19522.93411.2561.66274.1075-0.13284.4692-41.613838.7758-65.2808
71.094-1.15190.11773.9026-0.30471.9341.4182-3.76350.4264-0.54610.7130.01620.6-0.984-2.06221.8979-0.4477-0.21853.72510.40335.7989-38.665528.7954-67.2672
87.8289-6.476-1.9966.85943.82853.62111.35071.57251.1976-1.6292-0.7883-0.97870.0909-0.34110.59413.34082.5002-0.09994.601-0.35951.8977-34.756631.7704-58.7414
95.4695-3.36311.57115.08190.6264.10340.2816-1.00391.13950.1591-0.7327-1.47160.74980.8090.24791.0551-0.2412-0.25911.46930.37761.992160.044245.061612.0342
100.96181.78971.66185.12360.71786.042-1.2555-0.67931.1224-0.4194-1.26110.87050.2689-2.43031.56322.18770.1148-0.35881.794-1.19074.106926.096449.718715.3168
114.6332.81890.85713.52270.6830.15231.1701-0.89761.7102-0.5568-0.0118-0.3669-2.0484-1.7834-0.17512.9877-0.03670.29353.2780.09992.0168-2.366436.4351-85.7069
121.9764-0.80381.49422.66390.9374.2153-0.54571.52251.5369-1.0610.5154-0.2467-2.17530.21480.54641.9334-0.3529-0.3582.64240.65791.0703-15.519627.7148-72.2335
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 163)
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 164 THROUGH 277 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 278 THROUGH 384 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 385 THROUGH 745 )
5X-RAY DIFFRACTION5CHAIN 'V' AND (RESID 157 THROUGH 169 )
6X-RAY DIFFRACTION6CHAIN 'V' AND (RESID 170 THROUGH 174 )
7X-RAY DIFFRACTION7CHAIN 'V' AND (RESID 175 THROUGH 184 )
8X-RAY DIFFRACTION8CHAIN 'V' AND (RESID 185 THROUGH 193 )
9X-RAY DIFFRACTION9CHAIN 'R' AND (RESID 17 THROUGH 39 )
10X-RAY DIFFRACTION10CHAIN 'R' AND (RESID 40 THROUGH 102 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 1 THROUGH 97 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 17 THROUGH 112 )

+
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