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- PDB-9x7e: Crystal of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with n... -

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Basic information

Entry
Database: PDB / ID: 9x7e
TitleCrystal of CCoV-HuPn-2018 3CL protease (3CLpro) in complex with nirmatrelvir
Components3C-like protease
KeywordsVIRAL PROTEIN / Protease / Mpro / Viral protein-inhibitor complex
Function / homology
Function and homology information


host cell membrane / viral genome replication / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methyltransferase cap1 activity ...host cell membrane / viral genome replication / endonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / viral protein processing / lyase activity / host cell perinuclear region of cytoplasm / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / NSP15, NendoU domain, coronavirus ...Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / 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. / 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
Similarity search - Domain/homology
Chem-4WI / ORF1ab polyprotein
Similarity search - Component
Biological speciesCanine coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsNie, T.Q. / Su, H.X. / Li, M.J. / Xu, Y.C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci / Year: 2025
Title: Structure-Based Development of Ultra-Broad-Spectrum 3C-Like Protease Inhibitors.
Authors: Su, H. / Nie, T. / Chen, G. / Xiong, M. / Zhang, Y. / Wu, G. / You, M. / Xie, H. / He, J. / Xiong, Y. / Hu, H. / Zhao, W. / Li, M. / Xiao, G. / Zhang, L. / Xu, Y.
History
DepositionOct 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 24, 2025Provider: repository / Type: Initial release

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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
C: 3C-like protease
D: 3C-like protease
E: 3C-like protease
F: 3C-like protease
G: 3C-like protease
H: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,80915
Polymers264,2988
Non-polymers3,5117
Water73941
1
A: 3C-like protease
C: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0784
Polymers66,0752
Non-polymers1,0032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-12 kcal/mol
Surface area23790 Å2
MethodPISA
2
B: 3C-like protease
hetero molecules

F: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0784
Polymers66,0752
Non-polymers1,0032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_456-x-1/2,y+1/2,-z+11
Buried area2190 Å2
ΔGint-14 kcal/mol
Surface area24270 Å2
MethodPISA
3
D: 3C-like protease
hetero molecules

G: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0784
Polymers66,0752
Non-polymers1,0032
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
Buried area2220 Å2
ΔGint-13 kcal/mol
Surface area23620 Å2
MethodPISA
4
E: 3C-like protease
H: 3C-like protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5763
Polymers66,0752
Non-polymers5021
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-11 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.988, 126.453, 159.802
Angle α, β, γ (deg.)90.00, 90.82, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
3C-like protease


Mass: 33037.262 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine coronavirus 2 / Gene: ORF1ab / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A8F2ZG71
#2: Chemical
ChemComp-4WI / (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide / PF-07321332, bound form / nirmatrelvir, bound form / Paxlovid, bound form


Mass: 501.542 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C23H34F3N5O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.06 Å3/Da / Density % sol: 59.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 12% PEG3350, 100 mM sodium malonate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.37→159.79 Å / Num. obs: 123016 / % possible obs: 95 % / Redundancy: 4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.113 / Rpim(I) all: 0.064 / Rrim(I) all: 0.13 / Χ2: 0.9 / Net I/σ(I): 7 / Num. measured all: 492647
Reflection shellResolution: 2.37→2.49 Å / % possible obs: 99.9 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.662 / Num. measured all: 80656 / Num. unique obs: 18819 / CC1/2: 0.897 / Rpim(I) all: 0.346 / Rrim(I) all: 0.749 / Χ2: 0.62 / Net I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→38.67 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3003 6167 5.02 %
Rwork0.2628 --
obs0.2648 122809 94.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→38.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15483 0 245 41 15769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316019
X-RAY DIFFRACTIONf_angle_d0.62321867
X-RAY DIFFRACTIONf_dihedral_angle_d16.9035253
X-RAY DIFFRACTIONf_chiral_restr0.0472526
X-RAY DIFFRACTIONf_plane_restr0.0032860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.390.42641960.34544062X-RAY DIFFRACTION100
2.39-2.420.39711970.32364137X-RAY DIFFRACTION100
2.42-2.450.38162240.31284025X-RAY DIFFRACTION100
2.45-2.480.38922080.31774100X-RAY DIFFRACTION100
2.48-2.520.36022140.31154028X-RAY DIFFRACTION100
2.52-2.550.39342200.30854107X-RAY DIFFRACTION100
2.55-2.590.38612210.31064037X-RAY DIFFRACTION100
2.59-2.620.3572020.30154082X-RAY DIFFRACTION100
2.62-2.670.40522380.29794009X-RAY DIFFRACTION99
2.67-2.710.38431650.30372911X-RAY DIFFRACTION72
2.71-2.760.3812280.30944077X-RAY DIFFRACTION99
2.76-2.810.38742210.29844014X-RAY DIFFRACTION99
2.81-2.860.36171780.30584093X-RAY DIFFRACTION99
2.86-2.920.37162040.31954043X-RAY DIFFRACTION99
2.92-2.980.36021870.3014027X-RAY DIFFRACTION99
2.98-3.050.34321940.31083997X-RAY DIFFRACTION98
3.05-3.130.3461990.29484051X-RAY DIFFRACTION98
3.13-3.210.37822100.29954005X-RAY DIFFRACTION97
3.21-3.310.36312230.28923929X-RAY DIFFRACTION96
3.31-3.410.31392090.28743931X-RAY DIFFRACTION96
3.41-3.530.31091850.27543514X-RAY DIFFRACTION86
3.53-3.660.29211830.27253374X-RAY DIFFRACTION93
3.68-3.840.31661890.26053778X-RAY DIFFRACTION94
3.84-4.050.30121600.24553046X-RAY DIFFRACTION74
4.05-4.30.26212410.2263773X-RAY DIFFRACTION93
4.3-4.630.26081820.21723891X-RAY DIFFRACTION94
4.63-5.10.23092610.21773796X-RAY DIFFRACTION94
5.1-5.830.23851940.23863896X-RAY DIFFRACTION95
5.83-7.340.26022190.243947X-RAY DIFFRACTION95
7.34-38.670.22042150.21663962X-RAY DIFFRACTION94

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