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Basic information

Entry
Database: PDB / ID: 2a5k
TitleCrystal structures of SARS coronavirus main peptidase inhibited by an aza-peptide epoxide in space group P212121
Components3C-like peptidase
KeywordsHYDROLASE / cysteine peptidase / 3C-like / N-finger / chymotrypsin-like fold / long loop / alpha-helical domain / dimer / catalytic dyad / specificity pockets / aza-peptide epoxide / substrate-like inhibitor / C-S covalent bond / epoxide stereochemistry
Function / homology
Function and homology information


viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex ...viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex / mRNA capping enzyme complex / suppression by virus of host type I interferon production / positive regulation of RNA biosynthetic process / positive stranded viral RNA replication / protein K48-linked deubiquitination / : / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K63-linked deubiquitination / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / RNA-templated transcription / SARS-CoV-1 modulates host translation machinery / 7-methylguanosine mRNA capping / viral transcription / protein autoprocessing / positive regulation of viral genome replication / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / helicase activity / protein processing / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / ISG15-specific peptidase activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / DNA helicase / host cell cytoplasm / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / protein dimerization activity / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 / (+) 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 / Coronavirus 3Ecto domain profile. / : / 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 (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 / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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.
Similarity search - Domain/homology
Chem-AZP / Replicase polyprotein 1ab / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLee, T.-W. / Cherney, M.M. / Huitema, C. / Liu, J. / James, K.E. / Powers, J.C. / Eltis, L.D. / James, M.N.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal Structures of the Main Peptidase from the SARS Coronavirus Inhibited by a Substrate-like Aza-peptide Epoxide
Authors: Lee, T.-W. / Cherney, M.M. / Huitema, C. / Liu, J. / James, K.E. / Powers, J.C. / Eltis, L.D. / James, M.N.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN BEFORE BINDING TO THE PEPTIDASE, CBM, CBO AND OBN FORM AN EPOXIDE RING IN AZP. UPON ...HETEROGEN BEFORE BINDING TO THE PEPTIDASE, CBM, CBO AND OBN FORM AN EPOXIDE RING IN AZP. UPON BINDING TO THE PEPTIDASE, CYS145 SG NUCLEOPHILLICALLY ATTACKS CBM, RESULTING IN THE OPENING OF THE RING AND THE INVERSION OF THE CONFIGURATIONS OF CBM AND CBO.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3C-like peptidase
B: 3C-like peptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,1794
Polymers67,8952
Non-polymers1,2832
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.353, 67.478, 167.322
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3C-like peptidase / 3CL-PRO / 3CLp / NSP2


Mass: 33947.711 Da / Num. of mol.: 2 / Mutation: an additional Ala at the N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Strain: SARS / Plasmid: PT7HSP2 / Production host: Escherichia coli (E. coli) / Strain (production host): GJ1158
References: UniProt: P59641, UniProt: P0C6X7*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-AZP / (5S,8S,14R)-ETHYL 11-(3-AMINO-3-OXOPROPYL)-8-BENZYL-14-HYDROXY-5-ISOBUTYL-3,6,9,12-TETRAOXO-1-PHENYL-2-OXA-4,7,10,11-TETRAAZAPENTADECAN-15-OATE


Mass: 641.712 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H43N5O9
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium acetate, PEG 8000, ethylene glycol, dithiothreitol, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 33305 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.3→2.38 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2A5A
Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.506 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24889 1684 5.1 %RANDOM
Rwork0.17467 ---
obs0.1782 31565 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.452 Å2
Baniso -1Baniso -2Baniso -3
1-3.01 Å20 Å20 Å2
2---1.27 Å20 Å2
3----1.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4802 0 92 278 5172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9441.9666798
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5175612
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71623.913230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.85515825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1791532
X-RAY DIFFRACTIONr_chiral_restr0.1290.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023833
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.32347
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3330.53428
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2360.5479
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2920.346
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2840.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.60223113
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.52934946
X-RAY DIFFRACTIONr_scbond_it1.61622123
X-RAY DIFFRACTIONr_scangle_it2.28531852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 110 -
Rwork0.26 2153 -
obs--92.9 %

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