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Basic information

Entry
Database: PDB / ID: 6jij
TitleThe Crystal Structure of Main Protease from Mouse Hepatitis Virus A59 in Complex with an inhibitor
Components
  • 02J-ALA-VAL-LEU-PJE-010
  • Replicative polyprotein 1ab
KeywordsHYDRALASE/INHIBITOR / Main Protease / Mouse Hepatitis Virus A59 / HYDRALASE-INHIBITOR complex
Function / homology
Function and homology information


host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / omega peptidase activity ...host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / omega peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / symbiont-mediated suppression of host NF-kappaB cascade / endonuclease activity / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase 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 / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase activity / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / viral translational frameshifting / RNA-directed RNA polymerase / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / cysteine-type endopeptidase activity / viral RNA genome replication / DNA clamp loader activity / symbiont-mediated suppression of host gene expression / RNA-directed RNA polymerase activity / DNA-templated transcription / : / ATP hydrolysis activity / 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 / DNA2/NAM7-like helicase / AAA domain ...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 / DNA2/NAM7-like helicase / AAA domain / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface 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 / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / 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 / : / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / 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. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus
Similarity search - Domain/homology
N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE / Replicase polyprotein 1ab / ORF1ab polyprotein
Similarity search - Component
Biological speciesMurine coronavirus
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsCui, W. / Cui, S.S.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFD0500300 China
Ministry of Science and Technology (China)2015CB859800 China
National Natural Science Foundation of China31528006 China
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: The crystal structure of main protease from mouse hepatitis virus A59 in complex with an inhibitor.
Authors: Cui, W. / Cui, S. / Chen, C. / Chen, X. / Wang, Z. / Yang, H. / Zhang, L.
History
DepositionFeb 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_gen.oper_expression
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Replicative polyprotein 1ab
C: Replicative polyprotein 1ab
A: Replicative polyprotein 1ab
D: 02J-ALA-VAL-LEU-PJE-010
E: 02J-ALA-VAL-LEU-PJE-010
F: 02J-ALA-VAL-LEU-PJE-010


Theoretical massNumber of molelcules
Total (without water)101,2216
Polymers101,2216
Non-polymers00
Water19811
1
B: Replicative polyprotein 1ab
A: Replicative polyprotein 1ab
D: 02J-ALA-VAL-LEU-PJE-010
F: 02J-ALA-VAL-LEU-PJE-010


Theoretical massNumber of molelcules
Total (without water)67,4814
Polymers67,4814
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Replicative polyprotein 1ab
E: 02J-ALA-VAL-LEU-PJE-010

C: Replicative polyprotein 1ab
E: 02J-ALA-VAL-LEU-PJE-010


Theoretical massNumber of molelcules
Total (without water)67,4814
Polymers67,4814
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)167.787, 64.034, 117.953
Angle α, β, γ (deg.)90.00, 125.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Replicative polyprotein 1ab


Mass: 33059.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Murine coronavirus (strain A59) / Strain: A59 / Production host: Escherichia coli (E. coli) / References: UniProt: Q66WN6, UniProt: P0C6X9*PLUS
#2: Protein/peptide 02J-ALA-VAL-LEU-PJE-010


Type: Peptide-like / Class: Inhibitor / Mass: 680.791 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
References: N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
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: 2.59 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 0.1M Sodium acetate trihydrate (pH 4.4-4.6), 8%-10%(w/v) Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97854 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97854 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 29741 / % possible obs: 99.7 % / Redundancy: 3.3 % / Net I/σ(I): 15.2
Reflection shellResolution: 2.65→2.7 Å

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→36.96 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 31.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.27 1502 5.06 %
Rwork0.226 --
obs0.229 29710 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.65→36.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6991 0 0 11 7002
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047156
X-RAY DIFFRACTIONf_angle_d0.7729736
X-RAY DIFFRACTIONf_dihedral_angle_d13.5574126
X-RAY DIFFRACTIONf_chiral_restr0.051109
X-RAY DIFFRACTIONf_plane_restr0.0041243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.645-2.73040.38621230.30872435X-RAY DIFFRACTION95
2.7304-2.82790.34561260.29362564X-RAY DIFFRACTION99
2.8279-2.94110.36151400.27642536X-RAY DIFFRACTION100
2.9411-3.07490.30621370.28952576X-RAY DIFFRACTION100
3.0749-3.23690.29011310.27562569X-RAY DIFFRACTION100
3.2369-3.43960.32221450.27972555X-RAY DIFFRACTION100
3.4396-3.70490.30021160.25432586X-RAY DIFFRACTION100
3.7049-4.07740.26921500.23032585X-RAY DIFFRACTION100
4.0774-4.66640.26361310.19272568X-RAY DIFFRACTION100
4.6664-5.87530.24451450.19542589X-RAY DIFFRACTION100
5.8753-36.96470.20451580.17822645X-RAY DIFFRACTION99

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