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- PDB-8e7t: Crystal structure of Middle East respiratory syndrome coronavirus... -

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Basic information

Entry
Database: PDB / ID: 8e7t
TitleCrystal structure of Middle East respiratory syndrome coronavirus (MERS-CoV) 3CL protease inactive mutant C148A
Components3C-Like Protease
KeywordsVIRAL PROTEIN / MERS / Coronavirus / PROTEASE / DRUG RESISTANCE / HYDROLASE / DURG DISCOVERY / 3CL protease / inactive / inactive mutant
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 / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification ...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 / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / 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 / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / 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 ...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 / 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 / Trypsin-like serine proteases / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Thrombin, subunit H / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShaqra, A.M. / Zvornicanin, S.N. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Crystal structure of Middle East respiratory syndrome coronavirus (MERS-CoV) 3CL protease inactive mutant C148A
Authors: Shaqra, A.M. / Zvornicanin, S.N. / Schiffer, C.A.
History
DepositionAug 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: 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 Protease
B: 3C-Like Protease
C: 3C-Like Protease
D: 3C-Like Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,23218
Polymers133,2884
Non-polymers94414
Water9,962553
1
A: 3C-Like Protease
B: 3C-Like Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0829
Polymers66,6442
Non-polymers4377
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-25 kcal/mol
Surface area24660 Å2
MethodPISA
2
C: 3C-Like Protease
D: 3C-Like Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1519
Polymers66,6442
Non-polymers5067
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-27 kcal/mol
Surface area24370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.411, 90.010, 120.517
Angle α, β, γ (deg.)90.000, 108.328, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11D-581-

HOH

21D-582-

HOH

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Components

#1: Protein
3C-Like Protease


Mass: 33322.109 Da / Num. of mol.: 4 / Mutation: C148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome-related coronavirus
Production host: Escherichia coli (E. coli) / References: UniProt: W6A941
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / 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: 2.52 Å3/Da / Density % sol: 51.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10-20 % (w/v) PEG3350, 0.20-0.30 M NaCl, and 0.1 M Bis-Tris methane pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: May 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.5→24.93 Å / Num. obs: 45868 / % possible obs: 99.86 % / Redundancy: 7.3 % / Biso Wilson estimate: 29 Å2 / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.1909 / Rpim(I) all: 0.07489 / Rrim(I) all: 0.2055 / Net I/σ(I): 10.61
Reflection shellResolution: 2.5→2.589 Å / Redundancy: 7.4 % / Num. unique obs: 4543 / CC1/2: 0.675 / CC star: 0.898 / % possible all: 100

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Processing

Software
NameVersionClassification
CrysalisProdata collection
PHENIX1.19.2_4158refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WME

4wme


Resolution: 2.5→24.93 Å / SU ML: 0.3152 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2441 2000 4.36 %
Rwork0.1859 43865 -
obs0.1884 45865 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.83 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9051 0 59 553 9663
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00299688
X-RAY DIFFRACTIONf_angle_d0.573813267
X-RAY DIFFRACTIONf_chiral_restr0.0471497
X-RAY DIFFRACTIONf_plane_restr0.0051724
X-RAY DIFFRACTIONf_dihedral_angle_d17.09873323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.560.35131420.27333116X-RAY DIFFRACTION100
2.56-2.630.32141420.24243127X-RAY DIFFRACTION100
2.63-2.710.30571410.23853080X-RAY DIFFRACTION100
2.71-2.80.28371420.22733123X-RAY DIFFRACTION100
2.8-2.90.31091420.21623111X-RAY DIFFRACTION100
2.9-3.010.28651430.20693144X-RAY DIFFRACTION99.97
3.01-3.150.28411430.20353117X-RAY DIFFRACTION100
3.15-3.310.27141420.19253133X-RAY DIFFRACTION100
3.31-3.520.23381420.17233102X-RAY DIFFRACTION100
3.52-3.790.23031430.16253147X-RAY DIFFRACTION100
3.79-4.170.19691450.15423169X-RAY DIFFRACTION100
4.17-4.770.20761420.14333112X-RAY DIFFRACTION100
4.77-60.20591450.16873183X-RAY DIFFRACTION100
6-24.930.1991460.19033201X-RAY DIFFRACTION99.64

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