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- PDB-9ez4: Complex of a mutant of the SARS-CoV-2 main protease Mpro with the... -

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Basic information

Entry
Database: PDB / ID: 9ez4
TitleComplex of a mutant of the SARS-CoV-2 main protease Mpro with the nsp5/6 substrate peptide.
Components
  • GLY-VAL-THR-PHE-GLN-SER-ALA-VAL
  • Non-structural protein 7
  • Replicase polyprotein 1a
KeywordsHYDROLASE / SARS-CoV-2 / main protease / nsp5 / Cys-peptidase / 3CLpro
Function / homology
Function and homology information


viral genome replication / methyltransferase activity / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins ...viral genome replication / methyltransferase activity / protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / snRNP Assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / 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 toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methylation / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / 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 Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / 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 / (+)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 / 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 / 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.
Similarity search - Domain/homology
GLUTAMINE / DI(HYDROXYETHYL)ETHER / ORF1a polyprotein / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBattistutta, R. / Fornasier, E. / Giachin, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2024
Title: Allostery in homodimeric SARS-CoV-2 main protease.
Authors: Fornasier, E. / Fabbian, S. / Shehi, H. / Enderle, J. / Gatto, B. / Volpin, D. / Biondi, B. / Bellanda, M. / Giachin, G. / Sosic, A. / Battistutta, R.
History
DepositionApr 10, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase polyprotein 1a
B: Non-structural protein 7
C: GLY-VAL-THR-PHE-GLN-SER-ALA-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,35111
Polymers68,6823
Non-polymers6698
Water5,855325
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint2 kcal/mol
Surface area24360 Å2
Unit cell
Length a, b, c (Å)67.754, 99.036, 101.986
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 1 through 21 or resid 23...
d_2ens_1(chain "B" and (resid 1 through 21 or resid 23...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERTHRTHRAA1 - 211 - 21
d_12GLYGLYCYSCYSAA23 - 4423 - 44
d_13PROPROHISHISAA52 - 6452 - 64
d_14PHEPHELEULEUAA66 - 14166 - 141
d_15GLYGLYASPASPAA143 - 155143 - 155
d_16VALVALCYSCYSAA157 - 300157 - 300
d_21SERSERTHRTHRBB1 - 211 - 21
d_22GLYGLYHISHISBB23 - 6423 - 64
d_23PHEPHELEULEUBB66 - 14166 - 141
d_24GLYGLYASPASPBB143 - 155143 - 155
d_25VALVALCYSCYSBB157 - 300157 - 300

NCS oper: (Code: givenMatrix: (-0.227662839422, 0.678081298992, 0.698838596175), (0.692283507561, -0.391991921669, 0.60587612472), (0.684772353929, 0.621729913471, -0.38018250616)Vector: -11. ...NCS oper: (Code: given
Matrix: (-0.227662839422, 0.678081298992, 0.698838596175), (0.692283507561, -0.391991921669, 0.60587612472), (0.684772353929, 0.621729913471, -0.38018250616)
Vector: -11.9629433853, -12.0787550497, 25.1515346535)

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Replicase polyprotein 1a / ORF1a polyprotein


Mass: 33774.410 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: ORF1ab / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B1KJN1
#2: Protein Non-structural protein 7 / nsp7


Mass: 33726.410 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

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide GLY-VAL-THR-PHE-GLN-SER-ALA-VAL


Mass: 1181.342 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2

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Non-polymers , 4 types, 333 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M MMT (DL-malic acid, MES, and Tris base in molar ratio 1:2:2), pH 7.0, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.8→49.52 Å / Num. obs: 64002 / % possible obs: 99.5 % / Redundancy: 10.4 % / Biso Wilson estimate: 32.3 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.025 / Rrim(I) all: 0.081 / Rsym value: 0.077 / Net I/σ(I): 16.1
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.461 / Mean I/σ(I) obs: 1 / Num. unique obs: 3564 / CC1/2: 0.485 / Rpim(I) all: 0.603 / Rrim(I) all: 1.726

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.54 Å / SU ML: 0.2395 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9914
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2146 3172 4.96 %
Rwork0.1832 60744 -
obs0.1848 63916 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.38 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4689 0 43 325 5057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01344880
X-RAY DIFFRACTIONf_angle_d1.29466622
X-RAY DIFFRACTIONf_chiral_restr0.0797744
X-RAY DIFFRACTIONf_plane_restr0.0099860
X-RAY DIFFRACTIONf_dihedral_angle_d13.28721742
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.50602989305 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.35121250.3892453X-RAY DIFFRACTION93
1.83-1.860.35191340.32622542X-RAY DIFFRACTION97.59
1.86-1.890.31561340.27662575X-RAY DIFFRACTION97.38
1.89-1.920.2771250.25392598X-RAY DIFFRACTION99.96
1.92-1.950.2461580.21672592X-RAY DIFFRACTION99.57
1.95-1.990.26151350.20742637X-RAY DIFFRACTION99.96
1.99-2.030.25111320.19342616X-RAY DIFFRACTION99.93
2.03-2.080.24841470.20052631X-RAY DIFFRACTION100
2.08-2.120.21521190.192643X-RAY DIFFRACTION100
2.12-2.180.25461150.19332665X-RAY DIFFRACTION100
2.18-2.240.21821340.19682633X-RAY DIFFRACTION99.96
2.24-2.30.23591480.19652621X-RAY DIFFRACTION100
2.3-2.380.22281320.19192639X-RAY DIFFRACTION99.96
2.38-2.460.2221450.17552649X-RAY DIFFRACTION99.96
2.46-2.560.22341540.17812626X-RAY DIFFRACTION100
2.56-2.680.23591320.18082666X-RAY DIFFRACTION100
2.68-2.820.21261360.18732659X-RAY DIFFRACTION100
2.82-2.990.21461550.19362647X-RAY DIFFRACTION100
2.99-3.220.26291100.19542710X-RAY DIFFRACTION100
3.22-3.550.2091740.17412641X-RAY DIFFRACTION100
3.55-4.060.18141160.15822737X-RAY DIFFRACTION100
4.06-5.120.15381620.14162706X-RAY DIFFRACTION100
5.12-44.540.22971500.19232858X-RAY DIFFRACTION99.87
Refinement TLS params.Method: refined / Origin x: -2.91167295591 Å / Origin y: -2.71810716794 Å / Origin z: 16.6681188957 Å
111213212223313233
T0.176257211181 Å20.00116389444399 Å20.00485937462423 Å2-0.151301998459 Å2-0.0141351619045 Å2--0.220151609063 Å2
L0.646297574699 °2-0.00557819086716 °2-0.267171100753 °2-0.425218841664 °20.0202624256705 °2--2.07164889315 °2
S0.0118315129813 Å °0.057111763923 Å °0.0109430626581 Å °-0.044330657878 Å °-0.0364363372786 Å °-0.0460017682304 Å °-0.058021821676 Å °0.0834165936564 Å °0.0238268428876 Å °
Refinement TLS groupSelection details: all

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