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- PDB-9y8x: OC43 Mpro with EGT710 -

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Basic information

Entry
Database: PDB / ID: 9y8x
TitleOC43 Mpro with EGT710
Components3C-like proteinase
KeywordsHYDROLASE / Mpro Covid-19
Function / homology
Function and homology information


host cell membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / endonuclease activity / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / omega peptidase activity / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification ...host cell membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / endonuclease activity / 3'-5'-RNA exonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / omega peptidase activity / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / methyltransferase cap1 activity / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / single-stranded RNA binding / viral protein processing / lyase activity / host cell perinuclear region of cytoplasm / 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 / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, coronavirus HKU1-like / Coronavirus Nsp3 DPUP domain / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / NSP3, DPUP domain, murine hepatitis virus-like / Non-structural protein 2, MHV-like / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / AAA domain / Nonstructural protein 14, betacoronavirus ...RNA-dependent RNA polymerase, coronavirus HKU1-like / Coronavirus Nsp3 DPUP domain / Peptidase C30/C16, Betacoronavirus / Betacoronavirus, lineage A, NSP1 / NSP3, DPUP domain, murine hepatitis virus-like / Non-structural protein 2, MHV-like / Peptidase C16 family / Betacoronavirus, lineage A, NSP1 / AAA domain / 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 / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / 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 (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
Similarity search - Domain/homology
: / ORF1ab polyprotein
Similarity search - Component
Biological speciesHuman coronavirus OC43
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsKnapp, M.S. / Ornelas, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Npj Drug Discov / Year: 2025
Title: Preclinical characterization of EGT710, an oral non-peptidomimetic reversible covalent SARS-CoV-2 main protease inhibitor
Authors: Moquin, S.A. / Lakshminarayana, S.B. / Balavenkatraman, K.K. / Schiller, H. / Claas, A. / Bhhatarai, B. / Loisios-Konstantinidis, I. / Vulic, K. / Kurhade, C. / Kalveram, B.K. / Chen, J.Y.C. ...Authors: Moquin, S.A. / Lakshminarayana, S.B. / Balavenkatraman, K.K. / Schiller, H. / Claas, A. / Bhhatarai, B. / Loisios-Konstantinidis, I. / Vulic, K. / Kurhade, C. / Kalveram, B.K. / Chen, J.Y.C. / Zou, J. / Xie, X. / Tandeske, L. / Dovala, D. / Ornelas, E. / Knapp, M.S. / Fuller, D. / Nguyen, Z. / Barkan, D.T. / Bebrevska, L. / Wright, S.K. / Busby, S.A. / Blais, J. / Shi, P.Y. / Gaudet, S. / Bergeron, R. / Yu, H. / Zack, J. / Sarko, C. / Gu, F. / Bradner, J.E. / Tallarico, J.A. / Diagana, T.T. / Papillon, J.P.N.
History
DepositionSep 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8892
Polymers33,5031
Non-polymers3851
Water1,26170
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7774
Polymers67,0072
Non-polymers7712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2220 Å2
ΔGint-16 kcal/mol
Surface area24900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.77, 92.77, 69.771
Angle α, β, γ (deg.)90, 90, 90
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-564-

HOH

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Components

#1: Protein 3C-like proteinase


Mass: 33503.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus OC43 / Gene: Pp1ab / Production host: Escherichia coli (E. coli) / References: UniProt: U3M6R3
#2: Chemical ChemComp-A1CBU / (4S)-4-(iminomethyl)-3-(isoquinolin-4-yl)-1-[6-(trifluoromethyl)pyridin-3-yl]imidazolidin-2-one


Mass: 385.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14F3N5O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 0.2M NaSCN, 30% Peg 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.12→65.6 Å / Num. obs: 17868 / % possible obs: 100 % / Redundancy: 21 % / CC1/2: 0.999 / Net I/σ(I): 11.7
Reflection shellResolution: 2.12→2.23 Å / Num. unique obs: 2543 / CC1/2: 0.475

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→20.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.251 / SU Rfree Blow DPI: 0.206 / SU Rfree Cruickshank DPI: 0.204
RfactorNum. reflection% reflectionSelection details
Rfree0.265 866 -RANDOM
Rwork0.215 ---
obs0.2175 17757 99.7 %-
Displacement parametersBiso mean: 74.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.2861 Å20 Å20 Å2
2---0.2861 Å20 Å2
3---0.5722 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.12→20.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2255 0 28 70 2353
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082343HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.013192HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d769SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes415HARMONIC5
X-RAY DIFFRACTIONt_it2343HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion309SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1802SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion16.33
LS refinement shellResolution: 2.12→2.14 Å
RfactorNum. reflection% reflection
Rfree0.3916 21 -
Rwork0.3481 --
obs0.3504 413 95.49 %
Refinement TLS params.Origin x: -11.1653 Å / Origin y: 35.7497 Å / Origin z: -6.9061 Å
111213212223313233
T0.0534 Å20.0435 Å2-0.083 Å2--0.0911 Å2-0.0431 Å2--0.0088 Å2
L2.0792 °2-1.1318 °20.9342 °2-1.9251 °20.3613 °2--1.2926 °2
S-0.0672 Å °-0.2121 Å °-0.1688 Å °-0.2121 Å °-0.1968 Å °-0.0823 Å °-0.1688 Å °-0.0823 Å °0.264 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 297
2X-RAY DIFFRACTION1{ A|* }A301

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