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- PDB-8ykl: Crystal structure of MERS main protease in complex with X77 -

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Basic information

Entry
Database: PDB / ID: 8ykl
TitleCrystal structure of MERS main protease in complex with X77
ComponentsORF1a
KeywordsVIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / endonuclease activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / endonuclease activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / methylation / cysteine-type deubiquitinase activity / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / proteolysis / zinc ion binding / membrane
Similarity search - Function
Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / 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 / : ...Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / 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. / 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 / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsZhou, X.L. / Lin, C. / Zhang, J. / Li, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Crystal structures of coronaviral main proteases in complex with the non-covalent inhibitor X77.
Authors: Jiang, H. / Li, W. / Zhou, X. / Zhang, J. / Li, J.
History
DepositionMar 5, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ORF1a
B: ORF1a
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3604
Polymers65,4412
Non-polymers9192
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-15 kcal/mol
Surface area24970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.709, 94.876, 98.320
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

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Components

#1: Protein ORF1a


Mass: 32720.400 Da / Num. of mol.: 2 / Mutation: C148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: W5ZZG0
#2: Chemical ChemComp-X77 / N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-1H-imidazole-4-carboxamide


Mass: 459.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N5O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium formate, 0.1M BICINE pH8.5 20% PEG5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.93→36.94 Å / Num. obs: 55508 / % possible obs: 98.2 % / Redundancy: 5.1 % / Biso Wilson estimate: 28.3661025048 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.7
Reflection shellResolution: 1.93→2.04 Å / Rmerge(I) obs: 0.521 / Num. unique obs: 8001

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→36.94 Å / SU ML: 0.220685310159 / Cross valid method: FREE R-VALUE / σ(F): 1.33795957895 / Phase error: 23.0108253096
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.230093038165 2864 5.16734325665 %
Rwork0.200640719796 52561 -
obs0.202166698946 55425 98.1147105682 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.8685660534 Å2
Refinement stepCycle: LAST / Resolution: 1.93→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4558 0 68 187 4813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006840096012694740
X-RAY DIFFRACTIONf_angle_d0.9209405144876458
X-RAY DIFFRACTIONf_chiral_restr0.0547619836484731
X-RAY DIFFRACTIONf_plane_restr0.00565256813951821
X-RAY DIFFRACTIONf_dihedral_angle_d4.084139711472738
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9323-1.96560.2810499484631310.257053497032507X-RAY DIFFRACTION95.5797101449
1.9656-2.00140.287528422821270.247804711572654X-RAY DIFFRACTION99.179743224
2.0014-2.03990.256007053791520.2380746164532639X-RAY DIFFRACTION99.8211731044
2.0399-2.08150.2758469829631590.2258383290842602X-RAY DIFFRACTION99.8192335503
2.0815-2.12670.2305191789231250.2289096516932644X-RAY DIFFRACTION99.7837837838
2.1267-2.17620.2769260683281550.2239080886472649X-RAY DIFFRACTION99.9643493761
2.1762-2.23060.26561082391260.2206134619832667X-RAY DIFFRACTION99.8569896317
2.2306-2.29090.259801969481210.2207778474862115X-RAY DIFFRACTION79.6579978625
2.2909-2.35830.2733190300551500.2110628731152635X-RAY DIFFRACTION99.8923959828
2.3583-2.43440.2414656925821400.2280028412442687X-RAY DIFFRACTION99.9646393211
2.4344-2.52140.2427046200751390.228324471342644X-RAY DIFFRACTION99.9281867145
2.5214-2.62240.2466275659331380.2328157123182673X-RAY DIFFRACTION99.9644381223
2.6224-2.74170.3030379113291850.2282688534112633X-RAY DIFFRACTION100
2.7417-2.88620.2338216249381420.2178426071882685X-RAY DIFFRACTION99.8587071706
2.8862-3.06690.2240765430631370.2253885348862678X-RAY DIFFRACTION99.8226950355
3.0669-3.30360.2703237426841530.2187349568892672X-RAY DIFFRACTION99.7880607559
3.3036-3.63580.2313609339461320.2007910437922613X-RAY DIFFRACTION95.7112970711
3.6358-4.16120.2000624599081290.1727102203752584X-RAY DIFFRACTION94.6945898778
4.1612-5.24030.1871296492441750.1499662433642717X-RAY DIFFRACTION99.7585374267
5.2403-36.940.1730336861841480.1673041082282863X-RAY DIFFRACTION99.3401517651

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