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Basic information

Entry
Database: PDB / ID: 1lvo
TitleStructure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain
ComponentsReplicase, hydrolase domainRNA-dependent RNA polymerase
KeywordsHYDROLASE / 3C like / corona / proteinase / chymotrypsin / cysteine histidine dyad / beta barrel
Function / homology
Function and homology information


RNA exonuclease activity / host cell membrane / DNA helicase activity / viral genome replication / methyltransferase activity / Lyases; Phosphorus-oxygen lyases / methylation / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment ...RNA exonuclease activity / host cell membrane / DNA helicase activity / viral genome replication / methyltransferase activity / Lyases; Phosphorus-oxygen lyases / methylation / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / : / 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 ...Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / : / 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 / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / 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. / Coronavirus 3Ecto domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / : / Coronavirus (CoV) Nsp2 middle domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / NSP1, globular domain, alpha/betacoronavirus / : / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus Nsp3a Ubl domain profile. / Coronavirus Nsp3d Ubl 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. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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 / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Replicase polyprotein 1ab / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesTransmissible gastroenteritis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 Å
AuthorsAnand, K. / Palm, G.J. / Mesters, J.R. / Siddell, S.G. / Ziebuhr, J. / Hilgenfeld, R.
Citation
Journal: EMBO J. / Year: 2002
Title: Structure of coronavirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-helical domain.
Authors: Anand, K. / Palm, G.J. / Mesters, J.R. / Siddell, S.G. / Ziebuhr, J. / Hilgenfeld, R.
#1: Journal: J.Gen.Virol. / Year: 2000
Title: Virus-encoded proteinases and proteolytic processing in the Nidovirales
Authors: Ziebuhr, J. / Snijder, E.J. / Gorbalenya, A.E.
History
DepositionMay 29, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replicase, hydrolase domain
B: Replicase, hydrolase domain
C: Replicase, hydrolase domain
D: Replicase, hydrolase domain
E: Replicase, hydrolase domain
F: Replicase, hydrolase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,83648
Polymers198,7406
Non-polymers4,09642
Water18,0691003
1
A: Replicase, hydrolase domain
B: Replicase, hydrolase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,70017
Polymers66,2472
Non-polymers1,45315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-82 kcal/mol
Surface area25990 Å2
MethodPISA
2
C: Replicase, hydrolase domain
D: Replicase, hydrolase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,62016
Polymers66,2472
Non-polymers1,37314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-125 kcal/mol
Surface area26150 Å2
MethodPISA
3
E: Replicase, hydrolase domain
F: Replicase, hydrolase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,51615
Polymers66,2472
Non-polymers1,26913
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-102 kcal/mol
Surface area25470 Å2
MethodPISA
4
A: Replicase, hydrolase domain
B: Replicase, hydrolase domain
hetero molecules

E: Replicase, hydrolase domain
F: Replicase, hydrolase domain
hetero molecules

C: Replicase, hydrolase domain
D: Replicase, hydrolase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,83648
Polymers198,7406
Non-polymers4,09642
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area20090 Å2
ΔGint-334 kcal/mol
Surface area73260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.82, 160.13, 88.96
Angle α, β, γ (deg.)90.00, 94.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is unclear (monomer or dimer); observed are three dimers in the asymmetric unit.

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Components

#1: Protein
Replicase, hydrolase domain / RNA-dependent RNA polymerase


Mass: 33123.398 Da / Num. of mol.: 6 / Fragment: residues 2879-3180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Transmissible gastroenteritis virus / Genus: Coronavirus / Gene: ORF1a / Plasmid: pMAL-c2 / Production host: Escherichia coli (E. coli) / Strain (production host): TB1 / References: UniProt: Q9IW06, UniProt: P0C6Y5*PLUS
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE / 1,4-Dioxane


Mass: 88.105 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H8O2
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1003 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.72 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 8.8
Details: ammonium sulphate, MPD, dioxane, hepes, pH 8.8, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112.5 mg/mlprotein1drop
212 mMTris-HCl1droppH7.5
3120 mM1dropNaCl
41 mMdithiothreitol1drop
50.1 mMEDTA1drop
6100 mMHEPES1reservoirpH8.8
71.8 Mammonium sulfate1reservoir
86 %MPD1reservoir
95 mMdithiothreitol1reservoir
104 %dioxane1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7A10.97487, 0.97845, 0.97848, 0.97864, 0.97874, 0.95583, 0.9080, 1.0022
SYNCHROTRONELETTRA 5.2R20.99983
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDSep 16, 2000null
MARRESEARCH2CCDDec 12, 2000null
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1nullMADMx-ray1
2nullSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.974871
20.978451
30.978481
40.978641
50.978741
60.955831
70.9081
81.00221
90.999831
ReflectionResolution: 1.96→50 Å / Num. all: 144731 / Num. obs: 134114 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.44 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 13.54
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.85 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 2.43 / Num. unique all: 5367 / % possible all: 73.1
Reflection
*PLUS
Lowest resolution: 50 Å / % possible obs: 98.9 % / Redundancy: 5.4 %
Reflection shell
*PLUS
% possible obs: 97 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.221 / Mean I/σ(I) obs: 4

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Processing

Software
NameVersionClassification
SnBv2.0phasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.96→27.42 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 4041 3 %RANDOM
Rwork0.21 ---
all0.21 144731 --
obs0.21 134114 92.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.8737 Å2 / ksol: 0.326703 e/Å3
Displacement parametersBiso mean: 46.9 Å2
Baniso -1Baniso -2Baniso -3
1-10.65 Å20 Å23.59 Å2
2---1.35 Å20 Å2
3----9.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.96→27.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13805 0 189 1054 15048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d1.16
LS refinement shellResolution: 1.96→2.08 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.371 614 3 %
Rwork0.309 20020 -
obs--85.4 %
Xplor file
Refine-IDSerial noTopol fileParam file
X-RAY DIFFRACTION1PROTEIN_CYO.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM
Refinement
*PLUS
Lowest resolution: 50 Å / Rfactor obs: 0.21 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.16

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