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- PDB-7mhk: Crystal Structure of Apo/Unliganded SARS-CoV-2 Main Protease (Mpr... -

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Basic information

Entry
Database: PDB / ID: 7mhk
TitleCrystal Structure of Apo/Unliganded SARS-CoV-2 Main Protease (Mpro) at 310 K
Components3C-like proteinase
KeywordsHYDROLASE / SARS-CoV-2 / Coronavirus / main protease / 3CLpro / Mpro / 310 K / physiological temperature / temperature / temperature series / multitemperature / multiconformer
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / exoribonuclease complex / viral RNA-directed RNA polymerase complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / 5'-3' RNA helicase activity ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / exoribonuclease complex / viral RNA-directed RNA polymerase complex / viral replication complex formation and maintenance / endopeptidase complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / mRNA cap binding complex / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Lyases; Phosphorus-oxygen lyases / positive regulation of RNA biosynthetic process / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific peptidase activity / SARS coronavirus main proteinase / suppression by virus of host type I interferon production / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / host cell endosome / host cell endoplasmic reticulum-Golgi intermediate compartment / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / protein K48-linked deubiquitination / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / 7-methylguanosine mRNA capping / RNA-templated transcription / viral transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / suppression by virus of host toll-like receptor signaling pathway / host cell Golgi apparatus / host cell endoplasmic reticulum / suppression by virus of host NF-kappaB cascade / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive stranded viral RNA replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive regulation of viral genome replication / suppression by virus of host TRAF activity / protein autoprocessing / cysteine-type peptidase activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / cysteine-type deubiquitinase activity / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / integral to membrane of host cell / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / DNA-templated transcription / host cell cytoplasm / protein dimerization activity / suppression by virus of host type I interferon-mediated signaling pathway / host cell nucleus / ATP hydrolysis activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / Viral (Superfamily 1) RNA helicase / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Non-structural protein NSP15, middle domain superfamily / Nonstructural protein 15, middle domain, coronavirus / Coronavirus replicase NSP15, N-terminal oligomerization / Coronavirus replicase NSP15, middle domain / Non-structural protein 14, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / RNA polymerase, N-terminal, coronavirus / Non-structural protein NSP16, coronavirus-like / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Coronavirus 2'-O-methyltransferase / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein 2, SARS-CoV-like / NSP1 globular domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Carbamoyl-phosphate synthase subdomain signature 2. / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Lipocalin signature. / : / : / : / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-M domain profile. / : / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / NSP1, globular domain, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C 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 replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / Coronavirus replicase NSP2, C-terminal / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP4, C-terminal / Non-structural protein NSP9 superfamily, coronavirus / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP8 / RNA synthesis protein NSP10, coronavirus / Coronavirus papain-like peptidase / Non-structural protein NSP9, coronavirus / Coronavirus endopeptidase C30 / Peptidase C16, coronavirus / Peptidase C30, coronavirus / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP6 / Non-structural protein NSP4, C-terminal, coronavirus
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9601 Å
AuthorsEbrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)133769 United States
Department of Energy (DOE, United States)National Virtual Biotechnology Laboratory (NVBL) United States
Department of Energy (DOE, United States)Coronavirus CARES Act United States
Department of Energy (DOE, United States)BNL LDRD 20-042 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
Department of Energy (DOE, United States)KP1605010 United States
CitationJournal: Biorxiv / Year: 2021
Title: The temperature-dependent conformational ensemble of SARS-CoV-2 main protease (M pro ).
Authors: Ebrahim, A. / Riley, B.T. / Kumaran, D. / Andi, B. / Fuchs, M.R. / McSweeney, S. / Keedy, D.A.
History
DepositionApr 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Apr 20, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / cell / chem_comp / citation_author / database_2 / entity / entity_src_gen / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / struct_asym / struct_conf / struct_conn / struct_keywords / struct_site / struct_site_gen / symmetry
Item: _cell.volume / _citation_author.identifier_ORCID ..._cell.volume / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.gene_src_common_name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_torsion.auth_comp_id / _pdbx_validate_torsion.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_percent_reflns_R_free / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.percent_reflns_obs / _reflns.B_iso_Wilson_estimate / _reflns.d_resolution_high / _reflns.d_resolution_low / _reflns.pdbx_number_measured_all / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_keywords.text / _symmetry.space_group_name_Hall
Description: Ligand identity
Details: X-ray fluorescence is consistent with the presence of Zn.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,0474
Polymers33,8261
Non-polymers2223
Water1,36976
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0948
Polymers67,6512
Non-polymers4436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4640 Å2
ΔGint-77 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.300, 54.290, 44.970
Angle α, β, γ (deg.)90.000, 102.120, 90.000
Int Tables number5
Space group name H-MC121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-667-

HOH

21A-669-

HOH

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Plasmid: pET29b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 22% PEG 4000, 100 mM HEPES pH 7.0, 3-5% DMSO

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Data collection

DiffractionMean temperature: 310 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 3, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.9601→43.9676 Å / Num. obs: 19444 / % possible obs: 99.8613 % / Redundancy: 6.5902 % / CC1/2: 0.9902 / Rmerge(I) obs: 0.1952 / Rpim(I) all: 0.0839 / Rrim(I) all: 0.213 / Net I/σ(I): 5.3964 / Num. measured all: 128140
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
1.9601-1.99391006.71011.80450.321664359590.35220.75061.9569
1.9939-2.03021006.7281.58610.465464329560.44750.65921.7199
2.0302-2.06921006.54871.46490.596563269660.47710.61921.5928
2.0692-2.11151006.3141.33120.832760939650.55160.5761.4533
2.1115-2.157499.89846.24011.12061.092161349830.58760.48481.2239
2.1574-2.207699.8956.79071.06451.251664589510.64560.44041.1533
2.2076-2.262899.89876.75250.90441.594266589860.80160.37530.9803
2.2628-2.323999.89386.50690.80251.882261239410.76940.3410.8733
2.3239-2.392399.89736.36070.74031.959861899730.79430.31880.8079
2.3923-2.46951007.0260.67992.459867459600.85160.2760.7345
2.4695-2.55781007.00410.56513.068768299750.88370.23020.6108
2.5578-2.66021006.93810.50433.529167239690.89630.20780.5461
2.6602-2.781299.8986.92130.45244.162467769790.92230.18670.49
2.7812-2.92781006.89390.35325.47767569800.95410.1460.3827
2.9278-3.111299.89526.7660.28576.915964489530.96710.11970.3102
3.1112-3.351499.90066.6090.22148.6956664210050.97820.0940.2409
3.3514-3.688599.69176.28450.16311.458660969700.98650.07090.1781
3.6885-4.221899.69456.15830.121914.734760299790.99220.05370.1335
4.2218-5.317699.49196.1410.09517.768460129790.99380.0420.1041
5.3176-43.978799.2186.14380.0918.5228623610150.98150.04150.0997

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia20.7.32-g2f242514-dials-3.0data reduction
DIALS3.0.0-gb83e1fce8data scaling
PHASER1.18.2_3874phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6YB7

6yb7


Resolution: 1.9601→43.9676 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2473 --
Rwork0.1979 --
obs0.2002 19426 99.77 %
Refinement stepCycle: final / Resolution: 1.9601→43.9676 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2367 0 21 76 2464
Biso mean--51.2 46.4 -
Num. residues----306
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9601-2.080.39431300.34933043100
2.08-2.240.32141450.29853089100
2.24-2.470.34191610.27883056100
2.47-2.830.31141580.24453094100
2.83-3.560.2421360.19753104100
3.56-43.96760.19641480.1494316299

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