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- PDB-7mpb: SARS Coronavirus-2 Main Protease 3CL-pro binding Ascorbate -

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Basic information

Entry
Database: PDB / ID: 7mpb
TitleSARS Coronavirus-2 Main Protease 3CL-pro binding Ascorbate
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Hydrolase / SARS Coronavirus-2 Main Protease / 3CL-PRO / 3CLP / SARS-COV-2 MAIN PROTEASE
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / 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 / endopeptidase complex / Maturation of replicase proteins / endoribonuclease complex ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / 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 / endopeptidase complex / Maturation of replicase proteins / endoribonuclease complex / mRNA cap methyltransferase complex / RNA phosphodiester bond hydrolysis, exonucleolytic / 5'-3' RNA helicase activity / mRNA cap binding complex / Transcription of SARS-CoV-2 sgRNAs / positive regulation of RNA biosynthetic process / Lyases; Phosphorus-oxygen lyases / Translation of Replicase and Assembly of the Replication Transcription Complex / mRNA methylation / modulation by virus of host autophagy / Replication of the SARS-CoV-2 genome / double membrane vesicle viral factory outer membrane / snRNP Assembly / suppression by virus of host translation / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / SARS coronavirus main proteinase / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / suppression by virus of host type I interferon production / host cell endosome / mRNA guanylyltransferase / cytoplasmic viral factory / induction by virus of catabolism of host mRNA / protein K48-linked deubiquitination / SARS-CoV-2 modulates host translation machinery / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / omega peptidase activity / 7-methylguanosine mRNA capping / RNA-templated transcription / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / viral transcription / suppression by virus of host NF-kappaB cascade / suppression by virus of host toll-like receptor signaling pathway / protein K63-linked deubiquitination / modulation by symbiont of host protein ubiquitination / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell endoplasmic reticulum / host cell Golgi apparatus / positive stranded viral RNA replication / suppression by virus of host TRAF-mediated signal transduction / positive regulation of viral genome replication / protein autoprocessing / mRNA (nucleoside-2'-O-)-methyltransferase activity / cysteine-type peptidase activity / mRNA (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / DNA helicase / cysteine-type deubiquitinase activity / 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 / RNA helicase / lyase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / suppression by virus of host gene expression / copper ion binding / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-dependent RNA polymerase activity / host cell cytoplasm / protein dimerization activity / DNA-templated transcription / lipid binding / suppression by virus of host type I interferon-mediated signaling pathway / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / protein homodimerization activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 14, betacoronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 14, betacoronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2-O-methyltransferase / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / 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 proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Viral (Superfamily 1) RNA helicase / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Non-structural protein NSP16, coronavirus-like / Coronavirus 2'-O-methyltransferase / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / NSP1 globular domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / Lipocalin signature. / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / Carbamoyl-phosphate synthase subdomain signature 2. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Coronavirus Nsp3 Y3 domain profile. / Betacoronavirus Nsp3c-M domain profile. / NSP1, C-terminal domain, betacoronavirus / 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 / Betacoronavirus (BetaCoV) Nsp1 C-terminal 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 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / 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. / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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
Similarity search - Domain/homology
ASCORBIC ACID / TRIFLUOROETHANOL / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPandey, S. / Malla, T.N. / Stojkovic, E.A. / Schmidt, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biorxiv / Year: 2021
Title: Vitamin C inhibits SARS coronavirus-2 main protease essential for viral replication
Authors: Malla, T.N. / Pandey, S. / Poudyal, I. / Aldama, L. / Feliz, D. / Noda, M. / Phillips, G.N. / Stojkovic, E.A. / Schmidt, M.
History
DepositionMay 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1696
Polymers69,6172
Non-polymers5524
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-6 kcal/mol
Surface area25010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.350, 67.460, 157.509
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 34808.582 Da / Num. of mol.: 2
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: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ETF / TRIFLUOROETHANOL / 2,2,2-Trifluoroethanol


Mass: 100.040 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C2H3F3O
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.06 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 15 % PEG 3350, 5 mmol/L ascorbate, and trifluoroethanol (4 %)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.03 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 30845 / % possible obs: 92.6 % / Redundancy: 5.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.2 / Net I/σ(I): 8.2
Reflection shellResolution: 2.3→2.42 Å / Num. unique obs: 4075 / CC1/2: 0.46

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6WQF

6wqf


Resolution: 2.3→29.97 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1496 4.85 %RANDOM
Rwork0.2099 ---
obs0.2116 30845 97.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→29.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 36 198 4972
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054880
X-RAY DIFFRACTIONf_angle_d1.0686635
X-RAY DIFFRACTIONf_dihedral_angle_d12.102671
X-RAY DIFFRACTIONf_chiral_restr0.162747
X-RAY DIFFRACTIONf_plane_restr0.006864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.34161200.3092224X-RAY DIFFRACTION83
2.37-2.460.35381220.29682458X-RAY DIFFRACTION91
2.46-2.560.29951460.27862640X-RAY DIFFRACTION98
2.56-2.670.31491490.26762699X-RAY DIFFRACTION100
2.67-2.810.32411180.24972734X-RAY DIFFRACTION100
2.81-2.990.27671500.24132684X-RAY DIFFRACTION99
2.99-3.220.25111350.2312737X-RAY DIFFRACTION100
3.22-3.540.27011340.21242731X-RAY DIFFRACTION100
3.55-4.060.22931490.1882745X-RAY DIFFRACTION100
4.06-5.110.18021280.16362788X-RAY DIFFRACTION100
5.11-29.970.21450.18272909X-RAY DIFFRACTION99

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