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- PDB-2q6d: Crystal structure of infectious bronchitis virus (IBV) main protease -

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Basic information

Entry
Database: PDB / ID: 2q6d
TitleCrystal structure of infectious bronchitis virus (IBV) main protease
ComponentsInfectious bronchitis virus (IBV) main protease
KeywordsHYDROLASE / coronavirus / IBV / main protease / 3C-Like proteinase
Function / homology
Function and homology information


cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 ...cysteine-type peptidase activity / Transferases; Transferring one-carbon groups; Methyltransferases / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / mRNA guanylyltransferase / omega peptidase activity / methyltransferase cap1 / endonuclease activity / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / main proteinase (3clpro) structure, domain 3 ...Nonstructural protein 14, gammacoronavirus / Nonstructural protein 15, middle domain, gammacoronavirus / Nonstructural protein 15, N-terminal, gammacoronavirus / RNA-dependent RNA polymerase, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 6, gammacoronavirus / Non-structural protein 2, gammacoronavirus / Non-structural protein 5, gammacoronavirus / Non-structural protein 2, IBV-like / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Viral (Superfamily 1) RNA helicase / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / NSP12 RNA-dependent RNA polymerase, coronavirus / : / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / 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 / Nonstructural protein 13, 1B domain, coronavirus / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / : / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Trypsin-like serine proteases / Papain-like viral protease, palm and finger domains, 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / 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. / 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 main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Thrombin, subunit H / Non-structural protein 3, X-domain-like
Similarity search - Domain/homology
Replicase polyprotein 1ab / 3C-like protease
Similarity search - Component
Biological speciesInfectious bronchitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, Molecular Replacement / Resolution: 2.35 Å
AuthorsXue, X.Y. / Yang, H.T. / Xue, F. / Bartlam, M. / Rao, Z.H.
CitationJournal: J.Virol. / Year: 2008
Title: Structures of two coronavirus main proteases: implications for substrate binding and antiviral drug design.
Authors: Xue, X. / Yu, H. / Yang, H. / Xue, F. / Wu, Z. / Shen, W. / Li, J. / Zhou, Z. / Ding, Y. / Zhao, Q. / Zhang, X.C. / Liao, M. / Bartlam, M. / Rao, Z.
History
DepositionJun 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Infectious bronchitis virus (IBV) main protease
B: Infectious bronchitis virus (IBV) main protease
C: Infectious bronchitis virus (IBV) main protease


Theoretical massNumber of molelcules
Total (without water)100,9083
Polymers100,9083
Non-polymers00
Water10,196566
1
A: Infectious bronchitis virus (IBV) main protease
B: Infectious bronchitis virus (IBV) main protease


Theoretical massNumber of molelcules
Total (without water)67,2722
Polymers67,2722
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Infectious bronchitis virus (IBV) main protease


Theoretical massNumber of molelcules
Total (without water)33,6361
Polymers33,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)118.900, 118.900, 270.862
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11C-472-

HOH

DetailsThe biological assembly is a dimer:monomer structure with the monomer's C terminus inserted into the active site of the dimer.

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Components

#1: Protein Infectious bronchitis virus (IBV) main protease / Fragment


Mass: 33635.949 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Infectious bronchitis virus / Genus: Coronavirus / Strain: M41 / Gene: M41 3C-like protease gene / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q3Y5H1, UniProt: P0C6Y3*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.74 Å3/Da / Density % sol: 55.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 5% PEG 4000, 12% 2-propanol, 0.1 M sodium cacodylate pH 6.5., VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONAPS 19-ID20.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDMar 4, 2007
SBC2CCDDec 12, 2005
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97951
ReflectionResolution: 2.35→50 Å / Num. all: 47480 / Num. obs: 47480 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.054
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 5.3 / Num. unique all: 4689 / % possible all: 99.8

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD, Molecular Replacement
Starting model: PDB entry 1P9S

1p9s


Resolution: 2.35→50 Å / Isotropic thermal model: Isotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 4648 -Random
Rwork0.226 ---
all0.227 45866 --
obs-45866 95.6 %-
Refinement stepCycle: LAST / Resolution: 2.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6951 0 0 566 7517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0094
X-RAY DIFFRACTIONc_angle_d1.62

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