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- PDB-7k1l: Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in th... -

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Basic information

Entry
Database: PDB / ID: 7k1l
TitleCrystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-2',3'-Vanadate
ComponentsUridylate-specific endoribonuclease
KeywordsVIRAL PROTEIN / SARS Corona virus 2 / endoribonuclease / COVID-19 / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / double membrane vesicle viral factory outer membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerization / Nonstructural protein 15, middle domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
ACETATE ION / URIDINE-2',3'-VANADATE / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKim, Y. / Maltseva, N. / Jedrzejczak, R. / Endres, M. / Welk, L. / Chang, C. / Michalska, K. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Commun Biol / Year: 2021
Title: Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2.
Authors: Kim, Y. / Wower, J. / Maltseva, N. / Chang, C. / Jedrzejczak, R. / Wilamowski, M. / Kang, S. / Nicolaescu, V. / Randall, G. / Michalska, K. / Joachimiak, A.
History
DepositionSep 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Oct 18, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3739
Polymers83,3142
Non-polymers1,0597
Water4,774265
1
A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
hetero molecules

A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
hetero molecules

A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,11927
Polymers249,9436
Non-polymers3,17621
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area24920 Å2
ΔGint-200 kcal/mol
Surface area83590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.832, 150.832, 110.734
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Uridylate-specific endoribonuclease / NSP15 endoribnuclease


Mass: 41657.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold
References: UniProt: P0DTD1, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 272 molecules

#2: Chemical ChemComp-UVC / URIDINE-2',3'-VANADATE


Mass: 343.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H12N2O9V / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.36 Å3/Da / Density % sol: 71.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16 % w/v Polyethylene glycol 4,000, 100 mM TRIS; pH 8.5, 200 mM Sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 66979 / % possible obs: 98.6 % / Redundancy: 7 % / Biso Wilson estimate: 42 Å2 / CC1/2: 0.975 / Rmerge(I) obs: 0.193 / Net I/σ(I): 10.8
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.308 / Mean I/σ(I) obs: 1.05 / Num. unique obs: 3067 / CC1/2: 0.479 / % possible all: 91.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6VWW

6vww


Resolution: 2.25→49.37 Å / Cross valid method: FREE R-VALUE / σ(F): 1.61 / Phase error: 29.6352
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1915 3363 5.06 %
Rwork0.1666 63079 -
obs0.1721 66442 97.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.72 Å2
Refinement stepCycle: LAST / Resolution: 2.25→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5483 0 64 265 5812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025660
X-RAY DIFFRACTIONf_angle_d0.49437688
X-RAY DIFFRACTIONf_chiral_restr0.0431880
X-RAY DIFFRACTIONf_plane_restr0.0028979
X-RAY DIFFRACTIONf_dihedral_angle_d19.45892071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.290.29171760.25562799X-RAY DIFFRACTION83.18
2.29-2.330.30861630.25812943X-RAY DIFFRACTION87.43
2.33-2.370.30181540.24453044X-RAY DIFFRACTION90.25
2.37-2.420.25081510.24963080X-RAY DIFFRACTION91.21
2.42-2.480.28021630.23993123X-RAY DIFFRACTION92.45
2.48-2.530.23111950.23193165X-RAY DIFFRACTION92.65
2.53-2.60.23121710.22483155X-RAY DIFFRACTION93.48
2.6-2.670.25581570.2213212X-RAY DIFFRACTION94.92
2.67-2.750.25121720.21993210X-RAY DIFFRACTION94.69
2.75-2.830.23382150.20253172X-RAY DIFFRACTION93.46
2.83-2.940.22881560.20183211X-RAY DIFFRACTION95.03
2.94-3.050.23982090.19223169X-RAY DIFFRACTION93.62
3.05-3.190.2031550.18163228X-RAY DIFFRACTION95
3.19-3.360.20441310.18033237X-RAY DIFFRACTION95.49
3.36-3.570.19051580.1633242X-RAY DIFFRACTION94.91
3.57-3.850.16741760.15183185X-RAY DIFFRACTION94.2
3.85-4.230.15891510.13473247X-RAY DIFFRACTION94.94
4.23-4.840.12771230.12513236X-RAY DIFFRACTION95.12
4.85-6.10.14671650.13153230X-RAY DIFFRACTION94
6.1-49.370.18271780.15873235X-RAY DIFFRACTION92.8
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)
15.18015554561-0.734543842583-1.306392554565.14041437121.131290804074.101776791010.02770724830080.172038926995-0.1276270268170.184145883721-0.0876044078156-0.322686731408-0.09655401833510.1511804015460.01017668929880.243624869416-0.0237985147858-0.009704738506650.2582461865920.01951047167120.450619282145-54.396683269740.9074139182-8.47816162451
21.176738204440.6024926318890.5443400651451.416155881041.042293401691.421944727350.1388869439730.0446423776726-0.4573489615970.09032617050780.0776363545957-0.3635830368130.2613214184250.130967397088-0.2035127169550.2714136803850.0166829234746-0.02292406354630.251295234212-0.02400270115090.670294419459-61.244330327720.1344889409-16.225217119
31.916452403150.1452528718031.268605330961.623897813590.07514640993991.61036779012-0.05735954873830.1164737438960.0659596394819-0.3533785590220.00819913042481-0.037903914846-0.1132499791780.04111038606610.04549855400150.379161387457-0.000253475619448-0.003920847917880.22400651255-0.03283039566010.605273781258-82.341690884822.1229005514-36.4365254694
41.13467150357-0.4278307639280.006435401062482.60742083264-0.1891031773960.756462756779-0.01884291618910.0766491806063-0.302659368861-0.05285377495940.002153638673540.3112661107130.0124562589868-0.08091020171510.0168677787570.3461929683420.0275883396864-0.002194580030160.266486893834-0.03389125044440.615053780551-87.896568924115.6997168436-31.3689294895
55.412470962911.14237286154-0.0789796728075.5920039536-2.245721284524.892400523790.0732883765758-0.08181252192280.0780367462759-0.0763527629268-0.01828188197240.521757146396-0.0164242508063-0.202651957522-0.09314092986240.2588479196230.02031576759410.01202685056120.24334389052-0.01475224935110.427338352691-91.870692649230.19954028777.8699847755
61.3488774258-0.3773839052490.615850212381.19616205659-0.6681018061881.026411609610.00970566551884-0.0139719011401-0.170398340393-0.00668165611714-0.022164801889-0.05424251925520.107755008064-0.03551418788620.01465065700360.2420943244880.002503984191330.02322522898550.202618888730.02179358182570.461803087855-75.17028277416.336512165415.3848555751
71.424139791741.872665040190.9202292034285.888174797854.799712743635.980435738750.308987591059-0.170028798866-0.08967028097260.352024094902-0.438078134959-0.1879058499170.309680962604-0.08829839907840.08753551449350.29200225327-0.024506801946-0.04578188097980.2731213012650.07709823940490.600093593253-63.558450204616.088688681527.0039163368
81.436718204180.9224822834740.6008570954093.488655019040.6207950359092.421026849610.0427660371526-0.179657060655-0.09243949284280.509374371705-0.0283648733608-0.3241365774530.1298270033040.0845734526984-0.02464959950240.400588894521-0.00703216962968-0.05893681357180.3418066377370.04497767486510.587076829212-55.029799302330.27630483235.5432968803
98.244985031623.492253467123.032722910284.714476284822.199884198275.072584444820.2669966078670.193513986984-0.03296322689590.1485987227110.408451000339-1.40609291106-0.2232761405760.808253174595-0.6471764535690.3632416515340.007356905138890.004599673256960.458145875231-0.01516477280970.996151140836-45.138417966524.712194313230.4194457489
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 38 )AA0 - 381 - 39
22chain 'A' and (resid 39 through 183 )AA39 - 18340 - 184
33chain 'A' and (resid 184 through 276 )AA184 - 276185 - 277
44chain 'A' and (resid 277 through 346 )AA277 - 346278 - 347
55chain 'B' and (resid 0 through 38 )BE0 - 381 - 39
66chain 'B' and (resid 39 through 183 )BE39 - 18340 - 184
77chain 'B' and (resid 184 through 203 )BE184 - 203185 - 204
88chain 'B' and (resid 204 through 325 )BE204 - 325205 - 326
99chain 'B' and (resid 326 through 346 )BE326 - 346327 - 347

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  • 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

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