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- PDB-7wqh: Crystal structure of HCoV-NL63 main protease with PF07304814 -

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Basic information

Entry
Database: PDB / ID: 7wqh
TitleCrystal structure of HCoV-NL63 main protease with PF07304814
Components3C-like proteinase
KeywordsVIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / endonuclease activity / mRNA guanylyltransferase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity ...host cell membrane / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / endonuclease activity / mRNA guanylyltransferase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / methyltransferase cap1 / 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 / RNA helicase activity / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / lyase activity / RNA helicase / 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 / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 ...Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Trypsin-like serine proteases / 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
Similarity search - Domain/homology
Chem-80I / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHuman coronavirus NL63
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsZhong, F.L. / Zhou, X.L. / Lin, C. / Zeng, P. / Li, J. / Zhang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Basis of Main Proteases of Coronavirus Bound to Drug Candidate PF-07304814
Authors: Li, J. / Lin, C. / Zhou, X. / Zhong, F. / Zeng, P. / McCormick, P.J. / Jiang, H. / Zhang, J.
History
DepositionJan 25, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)65,7464
Polymers64,6412
Non-polymers1,1052
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-12 kcal/mol
Surface area24850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.094, 82.794, 64.423
Angle α, β, γ (deg.)90.000, 109.001, 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

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / M-PRO / nsp5 / p34


Mass: 32320.662 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human coronavirus NL63 / Gene: rep, 1a-1b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P0C6X5, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-80I / [(3~{S})-3-[[(2~{S})-2-[(4-methoxy-1~{H}-indol-2-yl)carbonylamino]-4-methyl-pentanoyl]amino]-2-oxidanylidene-4-[(3~{R})-2-oxidanylidene-3,4-dihydropyrrol-3-yl]butyl] dihydrogen phosphate


Mass: 552.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H33N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate tribasic dihydrate, 16% w/v Polyethylene glycol 3350, pH5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979137 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979137 Å / Relative weight: 1
ReflectionResolution: 2.32→59.66 Å / Num. obs: 25391 / % possible obs: 93.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 40.8932995056 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 7.9
Reflection shellResolution: 2.32→2.45 Å / Rmerge(I) obs: 0.577 / Num. unique obs: 3867

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7E6L

7e6l


Resolution: 2.32→37.0239 Å / SU ML: 0.334625280692 / Cross valid method: NONE / σ(F): 1.33793583676 / Phase error: 29.6211162422
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2646373731 3726 7.88972176344 %
Rwork0.203883248774 43500 -
obs0.208654580782 25329 88.5111327686 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.4087182573 Å2
Refinement stepCycle: LAST / Resolution: 2.32→37.0239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 76 35 4469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007183515584354541
X-RAY DIFFRACTIONf_angle_d0.9010359271926200
X-RAY DIFFRACTIONf_chiral_restr0.0551345817814707
X-RAY DIFFRACTIONf_plane_restr0.00498623400849795
X-RAY DIFFRACTIONf_dihedral_angle_d5.53436768952536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.34920.3295069982051470.2911967743431716X-RAY DIFFRACTION96.6787752984
2.3492-2.38010.329585478221530.2642253994991787X-RAY DIFFRACTION96.7581047382
2.3801-2.41270.3165020539851350.2769156612771803X-RAY DIFFRACTION97.7800201816
2.4127-2.44710.3407286823121690.2784235176851739X-RAY DIFFRACTION96.6565349544
2.4471-2.48370.3405593282291610.2638188426111769X-RAY DIFFRACTION96.7903711133
2.4837-2.52250.3188328891021460.2589624443261735X-RAY DIFFRACTION95.6278596848
2.5225-2.56380.3330593848661450.2544485353741754X-RAY DIFFRACTION96.5920651068
2.5638-2.6080.3567000020851350.2515942112531765X-RAY DIFFRACTION95.6696878147
2.608-2.65540.3459614438831660.2629563767191708X-RAY DIFFRACTION94.3130347257
2.6554-2.70650.469393076563270.278814024033395X-RAY DIFFRACTION21.70781893
2.7065-2.76170.3066782222111550.245367682611760X-RAY DIFFRACTION95.4636091725
2.7617-2.82170.3231126557561500.2459598523061738X-RAY DIFFRACTION95.4017180394
2.8217-2.88730.279876177141400.2376739008741761X-RAY DIFFRACTION96.6446365023
2.8873-2.95950.3152672783131480.2303200984011773X-RAY DIFFRACTION96.5326633166
2.9595-3.03950.2931574756831560.2282520455911726X-RAY DIFFRACTION96.6119096509
3.0395-3.12890.352187927941460.229919682421756X-RAY DIFFRACTION96.5482233503
3.1289-3.22980.3073594823951410.2293660530181759X-RAY DIFFRACTION95.429432446
3.2298-3.34520.3122316053221480.2219827217891712X-RAY DIFFRACTION92.8607089366
3.3452-3.4790.304208070161240.2294654630931470X-RAY DIFFRACTION81.2850586435
3.479-3.63730.3036940388271280.2205825298911424X-RAY DIFFRACTION79.9587841319
3.6373-3.82880.248218533728970.2028583404131116X-RAY DIFFRACTION60.4384653712
3.8288-4.06840.2147165953171030.2002465140651216X-RAY DIFFRACTION67.5025588536
4.0684-4.38210.2187988048921360.1635451302671534X-RAY DIFFRACTION84.3860535624
4.3821-4.82220.2023127343761410.1430576092671628X-RAY DIFFRACTION89.6149949341
4.8222-5.51810.2163268971341360.1590350065051669X-RAY DIFFRACTION90.5215646941
5.5181-6.94470.2291990498221530.1755307377941658X-RAY DIFFRACTION91.234256927
6.9447-37.02390.1826358781421400.1528271671741629X-RAY DIFFRACTION90.2551020408

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