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- PDB-6z2e: Crystal structure of SARS-CoV-2 Mpro in complex with the activity... -

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Basic information

Entry
Database: PDB / ID: 6z2e
TitleCrystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone
Components3C-like proteinase
KeywordsVIRAL PROTEIN / SARS-CoV-2 / main protease / activity-based probe / inhibitor
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell endosome / 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 / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / 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 / : ...RNA-dependent RNA polymerase, SARS-CoV-like / 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 / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / (+)RNA virus helicase core domain profile. / 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 / Carbamoyl-phosphate synthase subdomain signature 2. / 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 / 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 / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / 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.
Similarity search - Domain/homology
Chem-Q5T / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, L. / Hilgenfeld, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Union (EU)# 101003627 Germany
CitationJournal: To Be Published
Title: Crystal structure of SARS-CoV-2 Mpro in complex with the activity-based probe, biotin-PEG(4)-Abu-Tle-Leu-Gln-vinylsulfone
Authors: Zhang, L. / Hilgenfeld, R.
History
DepositionMay 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2021Group: Source and taxonomy / Structure summary / Category: entity / entity_name_com / entity_src_gen
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_name_com.name / _entity_src_gen.gene_src_common_name
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9135
Polymers33,8261
Non-polymers1,0874
Water4,179232
1
AAA: 3C-like proteinase
hetero molecules

AAA: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,82510
Polymers67,6512
Non-polymers2,1748
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+1/31
Buried area4250 Å2
ΔGint-78 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.083, 104.083, 91.246
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11AAA-402-

CL

21AAA-717-

HOH

31AAA-730-

HOH

41AAA-732-

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 / Production host: Escherichia coli (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-Q5T / (4~{S})-4-[[(2~{S})-2-[[(2~{S})-2-[[(2~{S})-2-[3-[2-[2-[2-[2-[5-[(3~{a}~{S},4~{R},6~{a}~{R})-2-oxidanylidene-3,3~{a},4,6~{a}-tetrahydro-1~{H}-thieno[3,4-d]imidazol-4-yl]pentanoylamino]ethoxy]ethoxy]ethoxy]ethoxy]propanoylamino]butanoyl]amino]-3,3-dimethyl-butanoyl]amino]-4-methyl-pentanoyl]amino]-6-methylsulfonyl-hexanamide


Mass: 993.282 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H80N8O13S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.12 M Ethylene glycols (0.3 M Diethylene glycol, 0.3 M Triethylene glycol, 0.3 M Tetraethylene glycol, 0.3 M Pentaethylene glycol), 0.1 M buffer system 2 (1.0 M Sodium HEPES, MOPS (acid), ...Details: 0.12 M Ethylene glycols (0.3 M Diethylene glycol, 0.3 M Triethylene glycol, 0.3 M Tetraethylene glycol, 0.3 M Pentaethylene glycol), 0.1 M buffer system 2 (1.0 M Sodium HEPES, MOPS (acid), pH 7.5), pH 7.5, 30% Precipitant mix 3 (20% glycerol, 10% PEG 4000)
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.7→45.62 Å / Num. obs: 32640 / % possible obs: 100 % / Redundancy: 38.5 % / CC1/2: 1 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.012 / Rrim(I) all: 0.075 / Net I/σ(I): 32.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 38 % / Rmerge(I) obs: 1.574 / Num. unique obs: 4679 / CC1/2: 0.861 / Rpim(I) all: 0.257 / Rrim(I) all: 1.595 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALA3.3.22data scaling
MOLREP11.7.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6Y2E

6y2e


Resolution: 1.7→45.247 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.939 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.12 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2434 1625 4.986 %
Rwork0.192 30969 -
all0.195 --
obs-32594 99.982 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 32.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.334 Å2-0.167 Å2-0 Å2
2---0.334 Å20 Å2
3---1.083 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 70 232 2670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132490
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172256
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.6763381
X-RAY DIFFRACTIONr_angle_other_deg1.4421.6215241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5135305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73823.223121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7515388
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.398151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9011511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022794
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02522
X-RAY DIFFRACTIONr_nbd_refined0.2170.2481
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22197
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21210
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.21109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2160
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0880.22
X-RAY DIFFRACTIONr_metal_ion_refined0.130.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.221
X-RAY DIFFRACTIONr_nbd_other0.2020.286
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1290.218
X-RAY DIFFRACTIONr_mcbond_it2.8813.2011223
X-RAY DIFFRACTIONr_mcbond_other2.8813.2011222
X-RAY DIFFRACTIONr_mcangle_it3.9194.8031527
X-RAY DIFFRACTIONr_mcangle_other3.9184.8041528
X-RAY DIFFRACTIONr_scbond_it3.5483.6811267
X-RAY DIFFRACTIONr_scbond_other3.4163.6831267
X-RAY DIFFRACTIONr_scangle_it5.1485.3621854
X-RAY DIFFRACTIONr_scangle_other5.1475.3621855
X-RAY DIFFRACTIONr_lrange_it6.89339.7982734
X-RAY DIFFRACTIONr_lrange_other6.82839.432686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3061140.272235X-RAY DIFFRACTION100
1.744-1.7920.3381070.2582220X-RAY DIFFRACTION100
1.792-1.8440.3151070.2322121X-RAY DIFFRACTION100
1.844-1.9010.2571080.2392073X-RAY DIFFRACTION100
1.901-1.9630.312950.2412028X-RAY DIFFRACTION100
1.963-2.0320.3261190.2331930X-RAY DIFFRACTION100
2.032-2.1080.3291030.2451872X-RAY DIFFRACTION100
2.108-2.1940.2881000.2291818X-RAY DIFFRACTION100
2.194-2.2920.243940.2261745X-RAY DIFFRACTION99.9457
2.292-2.4040.324850.211669X-RAY DIFFRACTION100
2.404-2.5340.285910.1961591X-RAY DIFFRACTION100
2.534-2.6870.221680.2071535X-RAY DIFFRACTION100
2.687-2.8730.262800.2011424X-RAY DIFFRACTION100
2.873-3.1030.233540.1891347X-RAY DIFFRACTION100
3.103-3.3980.243720.1871236X-RAY DIFFRACTION100
3.398-3.7990.223750.181120X-RAY DIFFRACTION100
3.799-4.3850.218460.161017X-RAY DIFFRACTION100
4.385-5.3670.189570.145860X-RAY DIFFRACTION100
5.367-7.5770.168340.162699X-RAY DIFFRACTION100

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