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- PDB-7wqj: Crystal structure of MERS main protease in complex with PF07304814 -

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Basic information

Entry
Database: PDB / ID: 7wqj
TitleCrystal structure of MERS main protease in complex with PF07304814
Components3C-like proteinase
KeywordsVIRAL PROTEIN/INHIBITOR / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / endonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification ...host cell membrane / viral genome replication / methyltransferase activity / endonuclease activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / methylation / omega peptidase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / viral protein processing / host cell perinuclear region of cytoplasm / 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 / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / Betacoronavirus single-stranded poly(A) binding domain / 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 ...Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / Betacoronavirus single-stranded poly(A) binding domain / 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 / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus replicase NSP1 / 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 / Thrombin, subunit H / 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 / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMiddle East respiratory syndrome-related coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsLin, C. / Zhang, J. / Li, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)66,0573
Polymers65,5052
Non-polymers5531
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-13 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.515, 92.771, 97.703
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 3C-like proteinase / Growth factor-like peptide / Leader protein / Non-structural protein 10 / Non-structural protein 2 ...Growth factor-like peptide / Leader protein / Non-structural protein 10 / Non-structural protein 2 / Non-structural protein 3 / Non-structural protein 4 / Non-structural protein 6 / Non-structural protein 7 / Non-structural protein 8 / Non-structural protein 9 / Papain-like proteinase / nsp5 / p65 homolog


Mass: 32752.463 Da / Num. of mol.: 2
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: T2BB45, ubiquitinyl hydrolase 1, SARS coronavirus main proteinase
#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.: 1 / Source method: obtained synthetically / Formula: C24H33N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.86 Å3/Da / Density % sol: 56.95 %
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: 0.979137 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: 2.75→67.2952 Å / Num. obs: 19794 / % possible obs: 98.5 % / Redundancy: 8.2 % / Biso Wilson estimate: 39.7892961122 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 9.2
Reflection shellResolution: 2.75→2.9 Å / Rmerge(I) obs: 0.867 / Num. unique obs: 2638

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Processing

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

7dra


Resolution: 2.75→67.2952 Å / SU ML: 0.411650301408 / Cross valid method: NONE / σ(F): 1.34653237461 / Phase error: 30.8063880764
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.289779155047 3676 10.0500314405 %
Rwork0.224280814497 32901 -
obs0.230885593192 19753 96.9800615124 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.4799772086 Å2
Refinement stepCycle: LAST / Resolution: 2.75→67.2952 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4494 0 38 33 4565
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01179165841084642
X-RAY DIFFRACTIONf_angle_d1.047492300586333
X-RAY DIFFRACTIONf_chiral_restr0.0541476005892729
X-RAY DIFFRACTIONf_plane_restr0.00560152217728805
X-RAY DIFFRACTIONf_dihedral_angle_d5.041086977232680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.78460.3391778887351180.32183845926910X-RAY DIFFRACTION70.6529209622
2.7846-2.82280.3384549963771080.319227866742963X-RAY DIFFRACTION73.6082474227
2.8228-2.86310.365491058731420.3100995178951157X-RAY DIFFRACTION90.5857740586
2.8631-2.90580.3956945318281430.3165101390691293X-RAY DIFFRACTION99.653018737
2.9058-2.95120.3750854465291470.3073525216721321X-RAY DIFFRACTION99.660556687
2.9512-2.99960.3810609836651380.3011970948181314X-RAY DIFFRACTION99.7252747253
2.9996-3.05140.4245329636911230.2829476751731322X-RAY DIFFRACTION99.7928176796
3.0514-3.10680.3705931430311620.2896652819661253X-RAY DIFFRACTION99.9293785311
3.1068-3.16660.3119366842331480.2538506770651336X-RAY DIFFRACTION99.9326599327
3.1666-3.23120.2924169697751220.2530634746991296X-RAY DIFFRACTION99.9295278365
3.2312-3.30150.339174944621530.233065245831313X-RAY DIFFRACTION99.863760218
3.3015-3.37830.3560746382521470.2306622405951303X-RAY DIFFRACTION99.8622589532
3.3783-3.46280.3102413099631470.2364779583641308X-RAY DIFFRACTION99.9313186813
3.4628-3.55640.300537317981550.2110150056271308X-RAY DIFFRACTION99.8634812287
3.5564-3.6610.2791327652841350.2136318709011299X-RAY DIFFRACTION99.860724234
3.661-3.77920.2604131504231560.2178246114091287X-RAY DIFFRACTION99.8615916955
3.7792-3.91420.2531568499691470.2072988624421302X-RAY DIFFRACTION99.4509265614
3.9142-4.07090.224500369231280.1943599270821301X-RAY DIFFRACTION99.7905027933
4.0709-4.25620.2301599309691580.1986138259751309X-RAY DIFFRACTION99.5251017639
4.2562-4.48050.246099480021280.1866550099471299X-RAY DIFFRACTION99.6508379888
4.4805-4.76120.2585842727591560.1764172209561295X-RAY DIFFRACTION99.5881949211
4.7612-5.12870.2748161251241400.1940036436321320X-RAY DIFFRACTION99.1847826087
5.1287-5.64460.2620574720291450.209811185181291X-RAY DIFFRACTION98.9662301861
5.6446-6.46080.2797410006251490.2150853058911259X-RAY DIFFRACTION98.945888967
6.4608-8.13770.2649215394941500.2031940850441282X-RAY DIFFRACTION98.4869325997
8.1377-67.29520.2625699011011310.2029572089761260X-RAY DIFFRACTION95.6013745704

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