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- PDB-7rc1: X-ray Structure of SARS-CoV main protease covalently modified by ... -

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Basic information

Entry
Database: PDB / ID: 7rc1
TitleX-ray Structure of SARS-CoV main protease covalently modified by compound GRL-0686
Components3C-like proteinase
KeywordsVIRAL PROTEIN / SARS-CoV / 3CLpro / mpro / 3CL / main / protease / inhibitor / covalent / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral genome replication / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / endonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / omega peptidase activity / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase activity / proteolysis / zinc ion binding / identical protein binding / membrane
Similarity search - Function
Non-structural protein 3, SUD-N macrodomain, SARS-CoV / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 / 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 / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / 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 / Peptidase family C16 domain profile. / : / : / Coronavirus replicase NSP7 / 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. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, 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 / Papain-like protease, thumb domain 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 replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-4IO / Replicase polyprotein 1a
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsMesecar, A.D. / Anson, B.A. / Ghosh, A.K. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: J.Med.Chem. / Year: 2021
Title: Indole Chloropyridinyl Ester-Derived SARS-CoV-2 3CLpro Inhibitors: Enzyme Inhibition, Antiviral Efficacy, Structure-Activity Relationship, and X-ray Structural Studies.
Authors: Ghosh, A.K. / Raghavaiah, J. / Shahabi, D. / Yadav, M. / Anson, B.J. / Lendy, E.K. / Hattori, S.I. / Higashi-Kuwata, N. / Mitsuya, H. / Mesecar, A.D.
History
DepositionJul 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7257
Polymers33,8771
Non-polymers8496
Water5,891327
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,45014
Polymers67,7532
Non-polymers1,69712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4350 Å2
ΔGint11 kcal/mol
Surface area26680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.726, 84.471, 53.495
Angle α, β, γ (deg.)90.000, 105.058, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
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-682-

HOH

21A-712-

HOH

31A-802-

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: 33876.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus
Gene: 1a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0C6U8, SARS coronavirus main proteinase
#2: Chemical ChemComp-4IO / 5-chloropyridin-3-yl 1-(3-nitrobenzene-1-sulfonyl)-1H-indole-5-carboxylate


Mass: 457.844 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H12ClN3O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY
Nonpolymer detailsThe inhibitor GRL-0686 reacts with Cys-145 to form a thioester bond in the active site. The ...The inhibitor GRL-0686 reacts with Cys-145 to form a thioester bond in the active site. The chlorpyridyl group leaves after the reaction.

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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: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% PEG 20,000, 0.05M MES 6.0, 1% MPD, 50mM KCl, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.63→31.82 Å / Num. obs: 56039 / % possible obs: 97.67 % / Redundancy: 7.2 % / Biso Wilson estimate: 27.57 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.05835 / Rpim(I) all: 0.02408 / Rrim(I) all: 0.0633 / Net I/σ(I): 23.62
Reflection shellResolution: 1.63→1.688 Å / Redundancy: 5 % / Rmerge(I) obs: 0.5505 / Mean I/σ(I) obs: 2 / Num. unique obs: 4949 / CC1/2: 0.938 / CC star: 0.984 / Rpim(I) all: 0.2451 / Rrim(I) all: 0.6047 / % possible all: 85.93

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V3M

3v3m


Resolution: 1.63→31.82 Å / SU ML: 0.1614 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2026
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2217 1991 3.57 %
Rwork0.1905 53847 -
obs0.1916 55838 97.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.47 Å2
Refinement stepCycle: LAST / Resolution: 1.63→31.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2371 0 43 327 2741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622540
X-RAY DIFFRACTIONf_angle_d0.76793466
X-RAY DIFFRACTIONf_chiral_restr0.0505386
X-RAY DIFFRACTIONf_plane_restr0.0056450
X-RAY DIFFRACTIONf_dihedral_angle_d18.7525352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.670.35981190.33053203X-RAY DIFFRACTION81.48
1.67-1.710.31711380.29813694X-RAY DIFFRACTION94.18
1.71-1.760.28991420.26183855X-RAY DIFFRACTION98.11
1.76-1.820.29891410.23183889X-RAY DIFFRACTION98.94
1.82-1.890.24581450.22553914X-RAY DIFFRACTION98.88
1.89-1.960.24491430.22123877X-RAY DIFFRACTION99.14
1.96-2.050.23151450.20673921X-RAY DIFFRACTION99.36
2.05-2.160.24751450.19793910X-RAY DIFFRACTION99.58
2.16-2.30.2121450.18633930X-RAY DIFFRACTION99.63
2.3-2.470.24141460.19113937X-RAY DIFFRACTION100
2.47-2.720.21361470.19123962X-RAY DIFFRACTION99.95
2.72-3.110.25391460.19083950X-RAY DIFFRACTION99.9
3.11-3.920.16711460.16643946X-RAY DIFFRACTION99.78
3.92-31.820.22521430.18213859X-RAY DIFFRACTION95.72
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.030535420240.519394920853-0.1588966270971.16103917828-0.2379088743332.3631993451-0.0107627554212-0.0161438506593-0.335531680737-0.0470244352559-0.0670303407583-0.1328640244420.2874948937150.250381326102-0.0002254770607780.3084342859730.05878856238280.02114391729930.2401473880860.02963358983190.3609351422812.62233627449-37.423291357321.5128175811
20.854184538112-0.734017142489-0.2805383856581.15195614913-1.11811231843.8410706767-0.424939127357-0.5466305925630.8007670020.7451147804950.0161695347846-1.06914744322-1.380360976310.9056124827390.09636811825750.4171204900320.19627784342-0.01111871843810.5721403207940.0832281786660.60382966633120.9792533218-35.0167640919.0901428115
30.123225843211-0.02386986507550.1138608454830.21895498426-0.4653415741881.0467260354-0.618337355239-0.394573978705-0.1982070381990.156404747122-0.1626359218930.0375759529472-0.06500266938760.302961410544-0.007685888323540.697187386171-0.1627620583580.2369035288011.59658688506-0.2185116695971.4823183711228.6177172537-28.248169646819.5920064264
40.379397334549-0.10559514090.2318401005920.3594361398130.18665480090.282626569762-0.362297251529-0.429960950223-0.6679768160110.1600642880150.075407558031-0.4637042675980.04533571795810.154981973012-0.0006669464189880.4716728768490.1973092923130.09710113092360.5602469717670.1285439802820.7115095429722.9797293153-42.912696991616.8935250047
50.4829211217610.4195370396950.2796235569380.3825167719020.197108406270.182393427734-0.114393414243-0.100983170388-0.7349213185410.2892593349430.0164590159231-0.008083592854360.2388737061710.543620169971-0.006908880377780.5318736854170.303065441890.1385424139580.4078343882110.146555185320.67822814310913.5091959991-46.446642094317.9783080936
60.03876053334110.02077137268660.01873895007250.06014322714390.02567422901960.0197296416645-0.4028331643370.009866422159-0.955811885011-0.522913124803-0.153473635415-0.2248739847760.7183036540460.435636972923-0.008329416093090.551423135960.1229271250790.1401106966660.271912535016-0.004348855712450.7198173498827.89466079173-47.844346531916.5366319933
70.01526734721230.03631614606080.0517407604120.05379733587510.04824994285050.0181852093995-0.02663520557410.719009280172-0.293829004443-0.914480090628-0.08034373122660.5933124163130.375437633096-0.253022333408-0.01294204971770.4032225790280.04608695896-0.02440932794070.309306361209-0.02780566486210.413178750665-0.623619154231-35.43603546239.37799842591
80.374296442844-0.0774296024543-0.3208860386950.6112788911990.3410501613910.349122983178-0.03919759274850.132975980204-0.1712324234790.116633181507-0.04847634103340.0457320214051-0.0131778126150.145700443478-0.0001871459820250.2667807594830.0386691060603-0.02465035706870.2695929685980.05130494577190.3209345761030.606853475743-29.264153918520.4011788739
90.2120614595360.0519284940688-0.2470934338810.5797051949410.5239591694830.6734829751650.08812889741910.178842085138-0.195778113838-0.0699665663369-0.1413773144910.1028929000720.21377214840.0649735632444-0.0002794811549630.2504605530980.0463776214685-0.0187291207040.2850792478210.06660738554670.295567078631.90448537364-25.935688253420.3156436382
100.0543767754938-0.00621884405756-0.09982631619740.1859404311890.04924225808230.149327202163-0.0978651572897-0.265693946912-0.03891762151010.4980472935010.01461200262850.139495898799-0.1698733935110.287241175742-3.32080283445E-50.3025119370450.0591254233652-0.02170267212920.4509024575910.02305335505550.3024103028277.84472239014-26.641665674424.2796965343
111.21301757263-1.06447198807-0.6997472609921.98254389737-0.8132137781932.192345640080.02456134122570.0399602134606-0.347593533682-0.04196169467510.00261520444078-0.09418360281590.03987609430260.1220036236950.0006989451889230.2648325919520.0587964608118-0.01706380871270.2853678508160.01932947520190.2890686688082.59317704411-29.883217902716.7048943859
120.602419380804-0.432761060873-0.02195865625640.963595471049-0.7718321309630.8741681534420.05765727873890.2263828631420.0374675902624-0.157845878089-0.169040158729-0.4829011319520.03432842132230.444940441183-0.0008391620139340.282480340740.08309585058840.02711281169340.4547945349750.09213573699640.38438843547713.7692373339-25.036639393411.7018027584
132.11269387846-0.01722859457170.3823988885182.62724692821-0.4037292313022.118506578410.09014004299010.1356410032480.3511193650780.07987386207450.03577749435990.20307954358-0.41763921081-0.2811103349080.0007788197974930.3728947366060.1555919293470.02406987498580.3652366979960.06705479095750.274972927721-12.5461448363-8.041699961558.14486795501
140.564154323652-0.6358941193060.06289983312220.9275465298790.0577995539150.1034102000460.0881392063056-0.4391152471650.820119542720.6004026858250.172631447209-0.266048249788-0.9969164872810.331192961114-0.004166990617260.8963522206030.1277522451680.1088356177680.645178938374-0.04701820103850.407376882352-13.1082648745-5.5965241148522.8433702752
150.1316534509150.395057086908-0.04210575664680.764822471621-0.01527471566140.437648508140.195689535793-0.02013897859940.0991100074230.258703355668-0.07342096020570.720385249942-0.0881706202746-0.4261531578830.0004116351932640.3922588184620.0848281822385-0.003857046985110.4797322794480.0667881379680.418244032595-15.5613782013-19.325056136815.0799125563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:38)
2X-RAY DIFFRACTION2(chain A and resid 39:46)
3X-RAY DIFFRACTION3(chain A and resid 47:51)
4X-RAY DIFFRACTION4(chain A and resid 52:69)
5X-RAY DIFFRACTION5(chain A and resid 70:85)
6X-RAY DIFFRACTION6(chain A and resid 86:97)
7X-RAY DIFFRACTION7(chain A and resid 98:108)
8X-RAY DIFFRACTION8(chain A and resid 109:118)
9X-RAY DIFFRACTION9(chain A and resid 119:135)
10X-RAY DIFFRACTION10(chain A and resid 136:147)
11X-RAY DIFFRACTION11(chain A and resid 148:173)
12X-RAY DIFFRACTION12(chain A and resid 174:196)
13X-RAY DIFFRACTION13(chain A and resid 197:275)
14X-RAY DIFFRACTION14(chain A and resid 276:286)
15X-RAY DIFFRACTION15(chain A and resid 287:306)

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