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Entry
Database: PDB / ID: 5rhc
TitlePanDDA analysis group deposition SARS-CoV-2 main protease fragment screen -- Crystal Structure of SARS-CoV-2 main protease in complex with Cov_HetLib053 (Mpro-x2119)
Components3C-like proteinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / viral RNA-directed RNA polymerase complex / exoribonuclease complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / endopeptidase complex / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex ...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 / viral RNA-directed RNA polymerase complex / exoribonuclease complex / endoribonuclease complex / Transcription of SARS-CoV-2 sgRNAs / endopeptidase complex / 5'-3' RNA helicase activity / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / positive regulation of RNA biosynthetic process / Lyases; Phosphorus-oxygen lyases / 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 / host cell endosome / 3'-5'-exoribonuclease activity / 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 / transcription, RNA-templated / 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 regulation of viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / positive stranded viral RNA replication / suppression by virus of host TRAF activity / protein autoprocessing / cysteine-type peptidase activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / DNA helicase activity / cysteine-type deubiquitinase activity / single-stranded RNA binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / protein processing / host cell perinuclear region of cytoplasm / viral protein processing / 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 / transcription, DNA-templated / suppression by virus of host type I interferon-mediated signaling pathway / host cell cytoplasm / protein dimerization activity / 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
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 14, betacoronavirus / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Coronavirus 2'-O-methyltransferase / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Coronavirus proofreading exoribonuclease / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Nonstructural protein 15, middle domain, coronavirus / Coronavirus RNA-dependent RNA polymerase, N-terminal / Non-structural protein NSP15, middle domain superfamily / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / RNA polymerase, N-terminal, coronavirus / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / Endoribonuclease EndoU-like / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Betacoronavirus SUD-C domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Non-structural protein NSP1 superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / (+)RNA virus helicase core domain profile. / (+) RNA virus helicase core domain / 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. / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP1, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Non-structural protein 6, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / 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 / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / 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 / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Non-structural protein NSP4, N-terminal, coronavirus / RNA synthesis protein NSP10, coronavirus / Coronavirus replicase NSP8 / Coronavirus endopeptidase C30 / Non-structural protein NSP8, coronavirus / Coronavirus papain-like peptidase / Non-structural protein 6, coronavirus / 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 NSP3, C-terminal / Non-structural protein NSP4, C-terminal, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Peptidase C30, domain 3, coronavirus
Similarity search - Domain/homology
(E)-1-(1H-imidazol-2-yl)methanimine / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.58 Å
AuthorsFearon, D. / Owen, C.D. / Douangamath, A. / Lukacik, P. / Powell, A.J. / Strain-Damerell, C.M. / Resnick, E. / Krojer, T. / Gehrtz, P. / Wild, C. ...Fearon, D. / Owen, C.D. / Douangamath, A. / Lukacik, P. / Powell, A.J. / Strain-Damerell, C.M. / Resnick, E. / Krojer, T. / Gehrtz, P. / Wild, C. / Aimon, A. / Brandao-Neto, J. / Carbery, A. / Dunnett, L. / Skyner, R. / Snee, M. / Keeley, A. / Keseru, G.M. / London, N. / Walsh, M.A. / von Delft, F.
CitationJournal: Nat Commun / Year: 2020
Title: Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
Authors: Douangamath, A. / Fearon, D. / Gehrtz, P. / Krojer, T. / Lukacik, P. / Owen, C.D. / Resnick, E. / Strain-Damerell, C. / Aimon, A. / Abranyi-Balogh, P. / Brandao-Neto, J. / Carbery, A. / ...Authors: Douangamath, A. / Fearon, D. / Gehrtz, P. / Krojer, T. / Lukacik, P. / Owen, C.D. / Resnick, E. / Strain-Damerell, C. / Aimon, A. / Abranyi-Balogh, P. / Brandao-Neto, J. / Carbery, A. / Davison, G. / Dias, A. / Downes, T.D. / Dunnett, L. / Fairhead, M. / Firth, J.D. / Jones, S.P. / Keeley, A. / Keseru, G.M. / Klein, H.F. / Martin, M.P. / Noble, M.E.M. / O'Brien, P. / Powell, A. / Reddi, R.N. / Skyner, R. / Snee, M. / Waring, M.J. / Wild, C. / London, N. / von Delft, F. / Walsh, M.A.
History
DepositionMay 16, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2020Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.2Feb 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)34,3898
Polymers33,8261
Non-polymers5647
Water5,891327
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,77916
Polymers67,6512
Non-polymers1,12814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5360 Å2
ΔGint6 kcal/mol
Surface area25460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.940, 52.891, 44.543
Angle α, β, γ (deg.)90.000, 103.070, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 3C-like proteinase / SARS-CoV-2 main protease / 3CL-PRO / 3CLp


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-USA / (E)-1-(1H-imidazol-2-yl)methanimine


Mass: 95.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 1.92 Å3/Da / Density % sol: 35.79 % / Mosaicity: 0 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 15% PEG 4K, 5% DMSO, 0.1M MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.913 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.913 Å / Relative weight: 1
ReflectionResolution: 1.58→55.05 Å / Num. obs: 34080 / % possible obs: 97.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 22.78 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.061 / Rrim(I) all: 0.116 / Net I/σ(I): 6.2 / Num. measured all: 120891 / Scaling rejects: 35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.58-1.612.91.126483216800.3290.8141.4010.993.5
8.51-55.053.60.0658902460.9890.0410.07717.898.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (29-NOV-2019)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6LU7

6lu7


Resolution: 1.58→55.01 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU R Cruickshank DPI: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.106 / SU Rfree Blow DPI: 0.102 / SU Rfree Cruickshank DPI: 0.098
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 1672 4.91 %RANDOM
Rwork0.1811 ---
obs0.1829 34065 96.8 %-
Displacement parametersBiso max: 70.41 Å2 / Biso mean: 23.94 Å2 / Biso min: 11.47 Å2
Baniso -1Baniso -2Baniso -3
1--3.8513 Å20 Å20.8114 Å2
2--1.0917 Å20 Å2
3---2.7595 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.58→55.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 31 327 2705
Biso mean--34.43 35.01 -
Num. residues----304
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d826SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes427HARMONIC5
X-RAY DIFFRACTIONt_it2455HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion317SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2732SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2455HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg3331HARMONIC20.99
X-RAY DIFFRACTIONt_omega_torsion3.99
X-RAY DIFFRACTIONt_other_torsion14.52
LS refinement shellResolution: 1.58→1.59 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.277 39 5.72 %
Rwork0.2187 643 -
all-682 -
obs--90.35 %

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