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- PDB-1p9s: Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design ... -

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Basic information

Entry
Database: PDB / ID: 1p9s
TitleCoronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs
ComponentsReplicase polyprotein 1ab
KeywordsHYDROLASE / SARS-CoV / HCoV / CORONAVIRUS / TGEV
Function / homology
Function and homology information


exonuclease activity / host cell membrane / DNA helicase activity / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / transferase activity / omega peptidase activity ...exonuclease activity / host cell membrane / DNA helicase activity / viral genome replication / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / Hydrolases; Acting on ester bonds / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Alphacoronavirus nsp1 domain superfamily / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Pectin lyase fold/virulence factor / P-type ATPase, transmembrane domain superfamily / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily ...Alphacoronavirus nsp1 domain superfamily / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Pectin lyase fold/virulence factor / P-type ATPase, transmembrane domain superfamily / 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 / 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. / 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 viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / Trypsin-like serine proteases / : / 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Thrombin, subunit H / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Replicase polyprotein 1a / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHuman coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsAnand, K. / Ziebuhr, J. / Wadhwani, P. / Mesters, J.R. / Hilgenfeld, R.
CitationJournal: Science / Year: 2003
Title: Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of anti-SARS Drugs
Authors: Anand, K. / Ziebuhr, J. / Wadhwani, P. / Mesters, J.R. / Hilgenfeld, R.
History
DepositionMay 12, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase polyprotein 1ab
B: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7994
Polymers66,6222
Non-polymers1762
Water57632
1
A: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3992
Polymers33,3111
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Replicase polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3992
Polymers33,3111
Non-polymers881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.356, 76.240, 73.477
Angle α, β, γ (deg.)90.00, 103.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 4

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNAA1 - 3001 - 300
2VALVALBB1 - 2991 - 299

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Components

#1: Protein Replicase polyprotein 1ab / 3CL-PRO


Mass: 33311.234 Da / Num. of mol.: 2 / Fragment: residue 2966-3265, 3C-like proteinase / Mutation: C-terminal deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus / Genus: Coronavirus / Strain: 229E / Gene: ORF1a / Plasmid details: derivative of pMal-c2 / Plasmid: pMal-Mpro / Production host: Escherichia coli (E. coli) / Strain (production host): TB1
References: UniProt: Q05002, UniProt: P0C6U2*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 10000, 1,6-hexanediol, DTT, HEPES, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 283K
Crystal grow
*PLUS
Temperature: 10 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
17.1 mg/mlprotein1drop
211 mMTris-HCl1droppH8.0
3200 mM1dropNaCl
40.1 mMEDTA1drop
51 mMdithiothreitol1drop
61 %1,6-hexanediol1drop
710 %PEG100001drop
820 %PEG100001reservoir
92 %1,6-hexanediol1reservoir
105 mMdithiothreitol1reservoir
1112 %dioxane1reservoir
12100 mMHEPES1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9801 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 2.54→70.71 Å / Num. all: 17709 / Num. obs: 17709 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 9.1
Reflection
*PLUS
Lowest resolution: 70.7 Å / % possible obs: 98.2 % / Num. measured all: 216984
Reflection shell
*PLUS
Highest resolution: 2.54 Å / Lowest resolution: 2.61 Å / Rmerge(I) obs: 0.412

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1LVO

1lvo


Resolution: 2.54→70.71 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.837 / SU B: 12.516 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R Free: 0.371 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27887 965 5.2 %RANDOM
Rwork0.19639 ---
obs0.20068 17709 98.22 %-
all-17709 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.781 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20.55 Å2
2---0.91 Å20 Å2
3---0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.54→70.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4589 0 12 32 4633
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0214708
X-RAY DIFFRACTIONr_bond_other_d0.0030.024136
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.926371
X-RAY DIFFRACTIONr_angle_other_deg1.10439601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5475597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1030.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025367
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02999
X-RAY DIFFRACTIONr_nbd_refined0.2520.31045
X-RAY DIFFRACTIONr_nbd_other0.270.34900
X-RAY DIFFRACTIONr_nbtor_other0.1020.52705
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.5200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.314
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3670.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3610.58
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.34322933
X-RAY DIFFRACTIONr_mcangle_it2.29534684
X-RAY DIFFRACTIONr_scbond_it1.39921775
X-RAY DIFFRACTIONr_scangle_it2.21431687
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4348 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.350.5
medium thermal0.832
LS refinement shellResolution: 2.54→2.606 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.384 57
Rwork0.246 1179
Refinement
*PLUS
Lowest resolution: 70.7 Å / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.8

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