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- PDB-4hi3: Crystal structure of dimeric R298A mutant of SARS coronavirus mai... -

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Basic information

Entry
Database: PDB / ID: 4hi3
TitleCrystal structure of dimeric R298A mutant of SARS coronavirus main protease
Components3C-like proteinase
KeywordsHYDROLASE / Chymotrypsin-like protein / protease / cytosol
Function / homology
Function and homology information


Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / modulation by virus of host autophagy / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / suppression by virus of host type I interferon production ...Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / modulation by virus of host autophagy / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / suppression by virus of host type I interferon production / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / G-quadruplex RNA binding / suppression by virus of host ISG15-protein conjugation / protein K48-linked deubiquitination / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / suppression by virus of host NF-kappaB cascade / viral transcription / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / positive stranded viral RNA replication / protein autoprocessing / viral genome replication / suppression by virus of host TRAF activity / ubiquitinyl hydrolase 1 / double-stranded RNA binding / thiol-dependent deubiquitinase / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / endonuclease activity / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / suppression by virus of host type I interferon-mediated signaling pathway / host cell cytoplasm / protein dimerization activity / endoplasmic reticulum membrane / zinc ion binding / integral component of membrane / identical protein binding / cytosol
Similarity search - Function
Non-structural protein 3, SUD-N macrodomain, SARS-CoV / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus SUD-C domain / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus ...Non-structural protein 3, SUD-N macrodomain, SARS-CoV / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus SUD-C domain / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus replicase NSP3, N-terminal / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-M domain profile. / Betacoronavirus replicase NSP1 / Non-structural protein NSP1, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3c-C domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Non-structural protein 6, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase family C16 domain profile. / Coronavirus replicase NSP7 / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, N-terminal / Coronavirus papain-like peptidase / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP4, C-terminal / Coronavirus endopeptidase C30 / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Peptidase C30, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP9, coronavirus / Peptidase C16, coronavirus / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Replicase polyprotein 1a
Similarity search - Component
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsWu, C.-G. / Chou, C.-Y.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Mechanism for controlling the monomer-dimer conversion of SARS coronavirus main protease.
Authors: Wu, C.G. / Cheng, S.C. / Chen, S.C. / Li, J.Y. / Fang, Y.H. / Chen, Y.H. / Chou, C.Y.
History
DepositionOct 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references

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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


Theoretical massNumber of molelcules
Total (without water)69,9862
Polymers69,9862
Non-polymers00
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-9 kcal/mol
Surface area26200 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)55.042, 59.444, 59.822
Angle α, β, γ (deg.)71.29, 73.40, 72.31
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.867849, -0.293218, -0.401075), (-0.312749, -0.304838, 0.89959), (-0.386039, 0.906144, 0.172849)50.68999, 11.23499, 10.19466
DetailsThere is a biological dimer in the asymmetric unit.

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Components

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


Mass: 34992.855 Da / Num. of mol.: 2 / Mutation: R298A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Gene: 1a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
References: UniProt: P0C6U8, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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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: 50.17 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG 300, 5% PEG 1000, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.09→30 Å / Num. all: 37715 / Num. obs: 35837 / % possible obs: 94.7 %
Reflection shellResolution: 2.09→2.16 Å / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1uk4
Resolution: 2.09→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.237 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24138 1878 5 %RANDOM
Rwork0.18987 ---
all0.19241 37715 --
obs0.19241 35837 94.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.236 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å21.8 Å2-1.84 Å2
2--1.46 Å2-1.22 Å2
3---1.29 Å2
Refinement stepCycle: LAST / Resolution: 2.09→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4646 0 0 266 4912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024750
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9476456
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2225599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83224.434212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.75515767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4341522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2731
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213616
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.199 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.314 241 -
Rwork0.255 4672 -
obs--83.9 %

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