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- PDB-7xjw: Crystal structure of canine coronavirus main protease in complex ... -

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Basic information

Entry
Database: PDB / ID: 7xjw
TitleCrystal structure of canine coronavirus main protease in complex with GC376
ComponentsORF1a polyprotein
KeywordsVIRAL PROTEIN/INHIBITOR / 3C-like proteinase / VIRAL PROTEIN-INHIBITOR COMPLEX
Function / homology
Function and homology information


host cell membrane / viral genome replication / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transferase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy ...host cell membrane / viral genome replication / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transferase activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / proteolysis / RNA binding / zinc ion binding / membrane
Similarity search - Function
Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / Papain-like protease, N-terminal domain superfamily, coronavirus / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus replicase NSP2, N-terminal ...Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / Papain-like protease, N-terminal domain superfamily, coronavirus / NSP1, globular domain, alpha/betacoronavirus / 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 / 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 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Chem-K36 / ORF1a polyprotein
Similarity search - Component
Biological speciesCanine coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsWang, Y.C. / Yang, C.S. / Hou, M.H. / Tsai, C.L. / Chiu, Y.F. / Chen, Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)109-2311-B241-001 Taiwan
CitationJournal: Int J Mol Sci / Year: 2022
Title: A Structural Comparison of SARS-CoV-2 Main Protease and Animal Coronaviral Main Protease Reveals Species-Specific Ligand Binding and Dimerization Mechanism.
Authors: Ho, C.Y. / Yu, J.X. / Wang, Y.C. / Lin, Y.C. / Chiu, Y.F. / Gao, J.Y. / Lai, S.J. / Chen, M.J. / Huang, W.C. / Tien, N. / Chen, Y.
History
DepositionApr 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation_author.identifier_ORCID
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: ORF1a polyprotein
B: ORF1a polyprotein
C: ORF1a polyprotein
D: ORF1a polyprotein
E: ORF1a polyprotein
F: ORF1a polyprotein
G: ORF1a polyprotein
H: ORF1a polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,47216
Polymers264,5878
Non-polymers3,8848
Water1,946108
1
A: ORF1a polyprotein
B: ORF1a polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1184
Polymers66,1472
Non-polymers9712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-13 kcal/mol
Surface area25580 Å2
MethodPISA
2
C: ORF1a polyprotein
D: ORF1a polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1184
Polymers66,1472
Non-polymers9712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-11 kcal/mol
Surface area25490 Å2
MethodPISA
3
E: ORF1a polyprotein
F: ORF1a polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1184
Polymers66,1472
Non-polymers9712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-12 kcal/mol
Surface area25710 Å2
MethodPISA
4
G: ORF1a polyprotein
H: ORF1a polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,1184
Polymers66,1472
Non-polymers9712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-15 kcal/mol
Surface area25490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.975, 125.749, 160.418
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-511-

HOH

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Components

#1: Protein
ORF1a polyprotein


Mass: 33073.426 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine coronavirus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2WXL6
#2: Chemical
ChemComp-K36 / (1S,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid / GC376 / GC376


Type: peptide-like / Mass: 485.551 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H31N3O8S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication, antivirus*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.97 Å3/Da / Density % sol: 58.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate, 0.1 M Bis Tris propane 7.0, 25 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.75→30 Å / Num. obs: 79392 / % possible obs: 99.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.036 / Net I/σ(I): 20.39
Reflection shellResolution: 2.75→2.85 Å / Rmerge(I) obs: 0.386 / Num. unique obs: 7891 / CC1/2: 0.914 / Rpim(I) all: 0.234 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F49

4f49


Resolution: 2.75→27.82 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.905 / Cross valid method: THROUGHOUT / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23276 3926 5.1 %RANDOM
Rwork0.21254 ---
obs0.21356 73326 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0.17 Å2
2--0.07 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.75→27.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18224 0 232 108 18564
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01318818
X-RAY DIFFRACTIONr_bond_other_d0.0360.01717334
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.64525446
X-RAY DIFFRACTIONr_angle_other_deg2.3721.57239872
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.56152366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31523.33889
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.04153119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9391579
X-RAY DIFFRACTIONr_chiral_restr0.050.22384
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0221541
X-RAY DIFFRACTIONr_gen_planes_other0.0070.024345
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_it4.1985.2749497
X-RAY DIFFRACTIONr_mcbond_other4.1985.2749496
X-RAY DIFFRACTIONr_mcangle_it6.6687.911852
X-RAY DIFFRACTIONr_mcangle_other6.6677.90111853
X-RAY DIFFRACTIONr_scbond_it3.845.5549321
X-RAY DIFFRACTIONr_scbond_other3.8425.5599292
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2168.20513556
X-RAY DIFFRACTIONr_long_range_B_refined9.61361.97620340
X-RAY DIFFRACTIONr_long_range_B_other9.61861.98620315
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.752→2.823 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 233 -
Rwork0.296 4128 -
obs--74.45 %

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