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- PDB-7rbs: The crystal structure of Papain-Like Protease of SARS CoV-2, C111... -

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Basic information

Entry
Database: PDB / ID: 7rbs
TitleThe crystal structure of Papain-Like Protease of SARS CoV-2, C111S mutant, in complex with human ISG15
Components
  • Papain-like protease
  • Ubiquitin-like protein ISG15
KeywordsHYDROLASE / covid-19 / coronavirus / SARS / CoV-2 / papain-like protease / ISG15 / IDP51000 / IDP52003 / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ISG15-protein conjugation / positive regulation of protein oligomerization / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions ...ISG15-protein conjugation / positive regulation of protein oligomerization / regulation of type II interferon production / NS1 Mediated Effects on Host Pathways / protein localization to mitochondrion / response to type I interferon / Modulation of host responses by IFN-stimulated genes / negative regulation of type I interferon-mediated signaling pathway / negative regulation of viral genome replication / RSV-host interactions / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / viral genome replication / positive regulation of erythrocyte differentiation / methyltransferase activity / integrin-mediated signaling pathway / Negative regulators of DDX58/IFIH1 signaling / Termination of translesion DNA synthesis / PKR-mediated signaling / DDX58/IFIH1-mediated induction of interferon-alpha/beta / response to virus / modification-dependent protein catabolic process / ISG15 antiviral mechanism / positive regulation of type II interferon production / protein tag activity / Interferon alpha/beta signaling / integrin binding / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 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 cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / endonuclease activity / SARS-CoV-2 modulates host translation machinery / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / defense response to virus / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase 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 / host cell endoplasmic reticulum membrane / defense response to bacterium / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / innate immune response / cysteine-type endopeptidase activity / lipid binding / ubiquitin protein ligase binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. ...: / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / 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. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Ubiquitin-like domain superfamily / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Ubiquitin-like protein ISG15 / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsOsipiuk, J. / Tesar, C. / Jedrzejczak, R. / Endres, M. / Wydorski, P. / Joachimiak, L. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: Nat Commun / Year: 2023
Title: Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin.
Authors: Wydorski, P.M. / Osipiuk, J. / Lanham, B.T. / Tesar, C. / Endres, M. / Engle, E. / Jedrzejczak, R. / Mullapudi, V. / Michalska, K. / Fidelis, K. / Fushman, D. / Joachimiak, A. / Joachimiak, L.A.
History
DepositionJul 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2May 31, 2023Group: 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 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Papain-like protease
B: Ubiquitin-like protein ISG15
C: Papain-like protease
D: Ubiquitin-like protein ISG15
E: Papain-like protease
F: Ubiquitin-like protein ISG15
G: Papain-like protease
H: Ubiquitin-like protein ISG15
I: Papain-like protease
J: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,48915
Polymers266,16210
Non-polymers3275
Water97354
1
A: Papain-like protease
B: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2983
Polymers53,2322
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-7 kcal/mol
Surface area21850 Å2
MethodPISA
2
C: Papain-like protease
D: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2983
Polymers53,2322
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-8 kcal/mol
Surface area21920 Å2
MethodPISA
3
E: Papain-like protease
F: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2983
Polymers53,2322
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-7 kcal/mol
Surface area21870 Å2
MethodPISA
4
G: Papain-like protease
H: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2983
Polymers53,2322
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-11 kcal/mol
Surface area21930 Å2
MethodPISA
5
I: Papain-like protease
J: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2983
Polymers53,2322
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2620 Å2
ΔGint-6 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.673, 220.870, 232.787
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Papain-like protease / Non-structural protein 3 / nsp3 / PL2-PRO / Papain-like proteinase / PL-PRO


Mass: 35927.695 Da / Num. of mol.: 5 / Mutation: C111S
Source method: isolated from a genetically manipulated source
Details: Three N-terminal residues (SNA) are expression tag
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DTC1, ubiquitinyl hydrolase 1
#2: Protein
Ubiquitin-like protein ISG15 / Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross- ...Interferon-induced 15 kDa protein / Interferon-induced 17 kDa protein / IP17 / Ubiquitin cross-reactive protein / hUCRP


Mass: 17304.764 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: Three N-terminal residues (SNA) are expression tag / Source: (gene. exp.) Homo sapiens (human) / Gene: ISG15, G1P2, UCRP / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05161
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.02 M MgCl2, 0.1 M HEPES buffer, 22% poly(acrylicacid sodium salt) 5100

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jun 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.98→48.99 Å / Num. obs: 78254 / % possible obs: 99.9 % / Redundancy: 6.7 % / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.089 / Rrim(I) all: 0.232 / Χ2: 1.485 / Net I/av σ(I): 12.6 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
3.03-3.086.92.181.2338930.3640.7310.92.3611.224100
3.08-3.146.91.72638610.4920.7091.8681.153100
3.14-3.26.91.43638540.5450.5911.5551.15100
3.2-3.266.81.15238820.660.4771.2481.181100
3.26-3.336.70.92538870.7540.3861.0031.181100
3.33-3.416.60.78838910.80.330.8551.229100
3.41-3.56.50.61238700.8450.2590.6661.279100
3.5-3.595.90.45238870.8960.2020.4961.349100
3.59-3.76.60.39138840.9360.1630.4241.42599.9
3.7-3.8270.35438900.9520.1440.3821.486100
3.82-3.956.90.28138780.970.1150.3041.574100
3.95-4.116.90.23439190.9780.0960.2541.651100
4.11-4.36.80.18138860.9830.0750.1961.734100
4.3-4.536.70.15339340.9840.0640.1661.748100
4.53-4.8160.13539060.9860.0590.1481.746100
4.81-5.1870.12839280.9910.0520.1381.782100
5.18-5.770.12339390.9910.050.1331.77599.9
5.7-6.526.70.11239560.9920.0470.1211.73999.9
6.52-8.216.40.08439760.9950.0350.0911.68399.8
8.21-48.996.40.0641330.9970.0260.0651.58699.7

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YVA

6yva


Resolution: 2.98→48.99 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.925 / SU B: 39.556 / SU ML: 0.299 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 3.633 / ESU R Free: 0.36 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 3786 4.8 %RANDOM
Rwork0.1951 ---
obs0.1971 74428 97.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 155.25 Å2 / Biso mean: 76.102 Å2 / Biso min: 29.29 Å2
Baniso -1Baniso -2Baniso -3
1-2.35 Å20 Å2-0 Å2
2---1.64 Å20 Å2
3----0.71 Å2
Refinement stepCycle: final / Resolution: 2.98→48.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18418 0 5 54 18477
Biso mean--142.74 52.79 -
Num. residues----2349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01318839
X-RAY DIFFRACTIONr_bond_other_d0.0030.01717711
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.6525545
X-RAY DIFFRACTIONr_angle_other_deg1.0891.57740857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5152341
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.30223.603891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.544153240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0531570
X-RAY DIFFRACTIONr_chiral_restr0.0420.22455
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0221356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024252
LS refinement shellResolution: 2.98→3.061 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.376 161 -
Rwork0.354 3499 -
obs--62.21 %
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)
10.7980.21940.2760.420.03740.2211-0.04330.01080.0664-0.0398-0.07690.00710.04970.03010.12020.22880.0285-0.00620.02870.02310.108154.880173.130341.4726
20.4371-0.15310.04061.68570.95022.33970.0778-0.0362-0.06040.07220.0109-0.01230.13210.0998-0.08870.24780.0011-0.03990.04780.05880.100761.704863.029761.6297
31.83320.1011-0.45850.35620.00620.3416-0.10910.1503-0.05920.0440.0595-0.0023-0.046-0.01320.04960.35990.04140.00810.0457-0.02040.035179.795239.82535.4223
42.41061.757-0.3252.324-0.72340.62690.1072-0.11020.03490.1132-0.0379-0.0819-0.07760.0035-0.06920.38880.0824-0.02010.0457-0.03270.063386.153848.596326.1272
51.1342-0.6637-0.02110.7105-0.18070.45250.09440.0542-0.1007-0.0148-0.01470.05170.0497-0.0276-0.07970.3174-0.0059-0.08230.0143-0.01330.060968.2913-11.741421.2381
62.8977-0.9815-1.45190.8849-0.09741.39510.1517-0.07920.1327-0.1111-0.0842-0.0229-0.05280.1045-0.06750.3123-0.0147-0.07440.0721-0.0470.085184.80173.834327.0788
70.2431-0.25370.2260.6777-0.73561.05790.0647-0.0237-0.0228-0.00990.04790.06840.01310.0051-0.11260.2959-0.0936-0.04620.05070.02070.087938.3211-10.402866.726
81.2519-0.46070.34642.96250.02241.1515-0.15030.09540.1479-0.04150.142-0.25550.1907-0.05510.00830.2255-0.06020.02340.0297-0.00540.042961.2101-9.388662.5735
90.30640.15390.40660.74030.44231.787-0.0739-0.06910.0173-0.0213-0.00930.0572-0.1095-0.20270.08320.17090.0374-0.01590.05440.04630.134129.102542.357579.2383
100.28370.4647-0.39671.4387-0.66332.8393-0.04690.0328-0.07520.1706-0.1081-0.10140.0806-0.00460.1550.2342-0.0217-0.03470.0730.02840.177646.654127.271983.859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 501
2X-RAY DIFFRACTION2B1 - 157
3X-RAY DIFFRACTION3C2 - 501
4X-RAY DIFFRACTION4D1 - 157
5X-RAY DIFFRACTION5E2 - 501
6X-RAY DIFFRACTION6F1 - 157
7X-RAY DIFFRACTION7G2 - 501
8X-RAY DIFFRACTION8H1 - 157
9X-RAY DIFFRACTION9I2 - 501
10X-RAY DIFFRACTION10J1 - 157

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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