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- PDB-7t2u: SARS-CoV2 3C-Like protease complexed with Nemo peptide -

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Basic information

Entry
Database: PDB / ID: 7t2u
TitleSARS-CoV2 3C-Like protease complexed with Nemo peptide
Components
  • 3C-Like Protease
  • NEMO peptide
KeywordsHYDROLASE / SARS CoV2 / 3C-Like protease / Nemo peptide.
Function / homology
Function and homology information


IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process ...IKBKB deficiency causes SCID / IKBKG deficiency causes anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) (via TLR) / IkappaB kinase complex / establishment of vesicle localization / linear polyubiquitin binding / transferrin receptor binding / IkBA variant leads to EDA-ID / NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 / RIP-mediated NFkB activation via ZBP1 / positive regulation of ubiquitin-dependent protein catabolic process / SUMOylation of immune response proteins / anoikis / K63-linked polyubiquitin modification-dependent protein binding / positive regulation of T cell receptor signaling pathway / TRAF6 mediated NF-kB activation / positive regulation of macroautophagy / polyubiquitin modification-dependent protein binding / signaling adaptor activity / canonical NF-kappaB signal transduction / ubiquitin ligase complex / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / TNFR1-induced NF-kappa-B signaling pathway / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / Activation of NF-kappaB in B cells / Regulation of TNFR1 signaling / TAK1-dependent IKK and NF-kappa-B activation / NOD1/2 Signaling Pathway / response to virus / PKR-mediated signaling / mitotic spindle / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / spindle pole / Interleukin-1 signaling / Ovarian tumor domain proteases / protein guanylyltransferase activity / Downstream TCR signaling / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / positive regulation of NF-kappaB transcription factor activity / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / T cell receptor signaling pathway / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / ER-Phagosome pathway / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / protein-containing complex assembly / symbiont-mediated perturbation of host ubiquitin-like protein modification / positive regulation of canonical NF-kappaB signal transduction / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / Ub-specific processing proteases / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / defense response to bacterium / inflammatory response / induction by virus of host autophagy / immune response / copper ion binding / protein heterodimerization activity
Similarity search - Function
C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus ...C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Lipocalin signature. / (+) 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 Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab / NF-kappa-B essential modulator
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWakatsuki, S. / Mathews, I.I. / Hameedi, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Nat Commun / Year: 2022
Title: Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.
Authors: Hameedi, M.A. / T Prates, E. / Garvin, M.R. / Mathews, I.I. / Amos, B.K. / Demerdash, O. / Bechthold, M. / Iyer, M. / Rahighi, S. / Kneller, D.W. / Kovalevsky, A. / Irle, S. / Vuong, V.Q. / ...Authors: Hameedi, M.A. / T Prates, E. / Garvin, M.R. / Mathews, I.I. / Amos, B.K. / Demerdash, O. / Bechthold, M. / Iyer, M. / Rahighi, S. / Kneller, D.W. / Kovalevsky, A. / Irle, S. / Vuong, V.Q. / Mitchell, J.C. / Labbe, A. / Galanie, S. / Wakatsuki, S. / Jacobson, D.
History
DepositionDec 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-Like Protease
B: 3C-Like Protease
E: NEMO peptide
C: 3C-Like Protease
F: NEMO peptide
D: 3C-Like Protease


Theoretical massNumber of molelcules
Total (without water)144,6026
Polymers144,6026
Non-polymers00
Water3,549197
1
A: 3C-Like Protease
B: 3C-Like Protease
E: NEMO peptide


Theoretical massNumber of molelcules
Total (without water)72,3013
Polymers72,3013
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-24 kcal/mol
Surface area25800 Å2
MethodPISA
2
C: 3C-Like Protease
F: NEMO peptide
D: 3C-Like Protease


Theoretical massNumber of molelcules
Total (without water)72,3013
Polymers72,3013
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-22 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.390, 67.710, 77.840
Angle α, β, γ (deg.)102.510, 89.910, 107.390
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3C-Like Protease / 3CL-PRO / 3CLP / Main protease / Mpro


Mass: 35564.395 Da / Num. of mol.: 4 / Mutation: C145S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Protein/peptide NEMO peptide / NF-kappa-B essential modulator / NEMO / FIP-3 / IkB kinase-associated protein 1 / IKKAP1 / ...NF-kappa-B essential modulator / NEMO / FIP-3 / IkB kinase-associated protein 1 / IKKAP1 / Inhibitor of nuclear factor kappa-B kinase subunit gamma / I-kappa-B kinase subunit gamma / IKK-gamma / IKKG / IkB kinase subunit gamma / NF-kappa-B essential modifier


Mass: 1172.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKG, FIP3, NEMO / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y6K9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 20% PEG3350, 0.1M Bis-Tris (pH 6.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2021 / Details: Flat Si Rh coated Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.1→38.12 Å / Num. obs: 67720 / % possible obs: 96.4 % / Redundancy: 3.529 % / Biso Wilson estimate: 42.783 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.115 / Χ2: 0.856 / Net I/σ(I): 8.86 / Num. measured all: 239009 / Scaling rejects: 16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.1-2.153.6280.9241.7818099520049890.6031.08695.9
2.15-2.213.5780.7312.2117360503748520.6860.8696.3
2.21-2.283.5220.6542.4716787495647660.6960.77396.2
2.28-2.353.330.5532.7615411481346280.7390.66396.2
2.35-2.423.2890.4653.214592461344360.7950.55896.2
2.42-2.513.6710.3814.2215946450343440.8770.44796.5
2.51-2.63.7220.3145.0915540431841750.910.36796.7
2.6-2.713.7040.2585.9215003418340500.9380.30296.8
2.71-2.833.6580.2017.1413995394338260.9580.23697
2.83-2.973.6220.1538.7413434383737090.9730.17996.7
2.97-3.133.5670.11910.1912530364335130.9820.14196.4
3.13-3.323.3520.09711.211076342033040.9850.11796.6
3.32-3.553.1350.07513.099757325331120.9880.09295.7
3.55-3.833.6220.05917.1110398297128710.9930.06996.6
3.83-4.23.6090.05220.179684276426830.9940.06197.1
4.2-4.73.5850.04622.748579249023930.9940.05496.1
4.7-5.423.4860.04422.837321220721000.9950.05295.2
5.42-6.643.190.04719.935736187817980.9940.05795.7
6.64-9.393.5290.03926.914958143414050.9960.04698
9.39-38.123.6590.0333.1728037887660.9980.03697.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native protein

Resolution: 2.1→38.12 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.2999 / WRfactor Rwork: 0.2452 / FOM work R set: 0.734 / SU B: 8.688 / SU ML: 0.221 / SU R Cruickshank DPI: 0.3294 / SU Rfree: 0.2526 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.329 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2999 3386 5 %RANDOM
Rwork0.2451 ---
obs0.2479 64333 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.86 Å2 / Biso mean: 37.666 Å2 / Biso min: 9.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å2-0.51 Å2-1.18 Å2
2---0.27 Å20.13 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 2.1→38.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9530 0 0 204 9734
Biso mean---35.09 -
Num. residues----1232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0139767
X-RAY DIFFRACTIONr_bond_other_d0.0010.0159087
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.63913269
X-RAY DIFFRACTIONr_angle_other_deg1.1951.57620867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.92451226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.12723.224487
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.596151567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0041544
X-RAY DIFFRACTIONr_chiral_restr0.060.21272
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211262
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022326
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 248 -
Rwork0.354 4722 -
all-4970 -
obs--95.8 %

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