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- PDB-9cjp: X-ray crystal structure of SARS-CoV-2 main protease quadruple mut... -

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Basic information

Entry
Database: PDB / ID: 9cjp
TitleX-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Nirmatrelvir
Components3C-like proteinase nsp5
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR complex / SARS2
Function / homology
Function and homology information


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 / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway ...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 / ISG15-specific peptidase activity / TRAF3-dependent IRF activation pathway / 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 / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / symbiont-mediated suppression of host toll-like receptor signaling pathway / G-quadruplex RNA binding / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / 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 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / regulation of autophagy / 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
Chem-4WI / BROMIDE ION / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsEsler, M.A. / Shi, K. / Harris, R.S. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA214279 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R37 AI064064 United States
CitationJournal: To Be Published
Title: X-ray crystal structure of SARS-CoV-2 main protease quadruple mutants in complex with Nirmatrelvir
Authors: Esler, M.A. / Shi, K. / Harris, R.S. / Aihara, H.
History
DepositionJul 7, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 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: 3C-like proteinase nsp5
B: 3C-like proteinase nsp5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,11410
Polymers67,6512
Non-polymers1,4638
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-14 kcal/mol
Surface area25110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.095, 105.665, 53.100
Angle α, β, γ (deg.)90.000, 103.610, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 and (name CA or name...
d_2ens_1(chain "B" and ((resid 1 and (name CA or name...

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_11SERSERGLNGLNAA1 - 1271 - 127
d_12ALAALASERSERAA129 - 301129 - 301
d_134WI4WI4WI4WIAC401
d_21SERSERMETMETBB1 - 491 - 49
d_22ASNASNGLNGLNBB51 - 12751 - 127
d_23ALAALASERSERBB129 - 301129 - 301
d_244WI4WI4WI4WIBF401

NCS oper: (Code: givenMatrix: (-0.999969553315, -0.00737532460864, -0.00254892731357), (-0.00779338208095, 0.960423825864, 0.27843372265), (0.000394511435814, 0.27844511003, -0.960452062865)Vector: ...NCS oper: (Code: given
Matrix: (-0.999969553315, -0.00737532460864, -0.00254892731357), (-0.00779338208095, 0.960423825864, 0.27843372265), (0.000394511435814, 0.27844511003, -0.960452062865)
Vector: 16.1276811532, -4.35043870857, 29.7351020259)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 3C-like proteinase nsp5 / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.633 Da / Num. of mol.: 2 / Mutation: T21I, L50F, S144A, E166V
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

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Non-polymers , 5 types, 101 molecules

#2: Chemical ChemComp-4WI / (1R,2S,5S)-N-{(1E,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide / PF-07321332, bound form / nirmatrelvir, bound form / Paxlovid, bound form


Mass: 501.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H34F3N5O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antivirus, protease inhibitor*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: J309: 0.1 M Buffer System 3, pH 8.5, 0.09M NPS, 50% v/v Precipitant Mix 4, MD Morpheus MD1-47

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→52.83 Å / Num. obs: 32792 / % possible obs: 91.5 % / Redundancy: 3 % / Biso Wilson estimate: 29.32 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.047 / Rrim(I) all: 0.085 / Rsym value: 0.071 / Net I/σ(I): 6.1
Reflection shellResolution: 1.7→1.93 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 1640 / CC1/2: 0.785 / Rpim(I) all: 0.343 / Rrim(I) all: 0.585 / Rsym value: 0.47

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→52.83 Å / SU ML: 0.2276 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.6725
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2259 1619 4.94 %
Rwork0.18 31171 -
obs0.1822 32790 58.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.48 Å2
Refinement stepCycle: LAST / Resolution: 1.71→52.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4661 0 86 93 4840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00444856
X-RAY DIFFRACTIONf_angle_d0.72896615
X-RAY DIFFRACTIONf_chiral_restr0.0467750
X-RAY DIFFRACTIONf_plane_restr0.0065854
X-RAY DIFFRACTIONf_dihedral_angle_d13.63411729
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.680872578618 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.760.203720.33450X-RAY DIFFRACTION1.13
1.76-1.810.3685170.3271283X-RAY DIFFRACTION6.49
1.81-1.880.4229220.2942544X-RAY DIFFRACTION12.19
1.88-1.950.3301520.2701905X-RAY DIFFRACTION20.57
1.95-2.040.2777720.25471451X-RAY DIFFRACTION32.54
2.04-2.150.30621540.2512677X-RAY DIFFRACTION60.96
2.15-2.280.27351920.24143532X-RAY DIFFRACTION79.91
2.28-2.460.24562100.23244158X-RAY DIFFRACTION93.55
2.46-2.710.29622320.23024385X-RAY DIFFRACTION99.25
2.71-3.10.26562310.19934385X-RAY DIFFRACTION98.74
3.1-3.90.20312290.15824382X-RAY DIFFRACTION98.13
3.9-52.830.17012060.13244419X-RAY DIFFRACTION97.53
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)
11.743804055131.21014944575-0.2986781126722.25431904925-0.04635888934371.14751692650.140991156589-0.627626673221-0.2875533616780.1479007518310.1006293536940.4784926982020.627577291992-0.759523358783-0.008029537022550.286491814619-0.330024395209-0.08066216137680.7279901605190.397550155880.470901516099-8.67164578695-20.089574418822.7462311281
21.357068194160.729038458314-0.1034541262152.531192183250.3972216179141.802177250750.321968436395-0.67631581225-0.5209736173640.3223600326090.0348781129867-0.02516187328280.473307227207-0.453580729145-0.0259338228770.247124897738-0.149829760202-0.01349310960050.5011513589650.2320927773640.268392901074-0.205261857718-14.024174049325.7169913878
34.081942469170.5812853139751.459293773121.401904448770.3657468383512.82776437558-0.3700687193170.01842054189570.210833595891-0.02367242540930.174977697295-0.11107281041-0.3728388243560.1731393145390.1706503485940.231805706077-0.027542970043-0.009987959613920.45031905942-0.0002136424251950.17073272776214.88389624056.7937850828429.3125004266
41.657263733950.2402466295080.1038382323592.19491505742-0.2257434162462.199626502580.01681874815550.129199150261-0.374925829404-0.0914719525463-0.0474811484326-0.5509207095080.2140292161890.331727117545-0.01746537656290.113287849160.005492168421910.01965624838250.152970077760.006512330364490.32458232756122.142022101-16.76763585790.88332466716
53.49686234143-0.9257021721850.08384598109711.61764634853-0.2920499045580.71274943534-0.0250614771857-0.06443153002020.2048830357020.0268869761909-0.003486384953960.0653662858824-0.117739177632-0.006270191710170.02710698636030.153080779751-0.0321749694108-0.001907540052360.08975467399950.007920563137490.1584629883446.113768676174.905974139413.24265237525
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 76 )AA1 - 761 - 75
22chain 'A' and (resid 77 through 180 )AA77 - 18076 - 179
33chain 'A' and (resid 181 through 303 )AA181 - 303180 - 302
44chain 'B' and (resid 1 through 120 )BC1 - 1201 - 120
55chain 'B' and (resid 121 through 301 )BC121 - 301121 - 301

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