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- PDB-8e7n: Crystal structure of beluga whale Gammacoronavirus SW1 Mpro with ... -

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Basic information

Entry
Database: PDB / ID: 8e7n
TitleCrystal structure of beluga whale Gammacoronavirus SW1 Mpro with GC-376 captured in two conformational states
Componentsmain protease
KeywordsVIRAL PROTEIN / Gammacoronavirus / PROTEASE / DRUG RESISTANCE / COMPLEX / HYDROLASE / DURG DISCOVERY / MAIN PROTEASE / MPRO / SUBSTRATE COMPLEX / GC-376 / VIRAL PROTEIN-HYDROLASE-INHIBITOR complex / SW1 / Beluga Whale / Whale
Function / homology
Function and homology information


host cell membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / endonuclease activity / omega peptidase activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / viral protein processing ...host cell membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / endonuclease activity / omega peptidase activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / viral protein processing / host cell perinuclear region of cytoplasm / lyase activity / viral translational frameshifting / symbiont-mediated activation of host autophagy / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Non-structural protein 5, gammacoronavirus / DNA2/NAM7 helicase, helicase domain / AAA domain / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / NSP15, NendoU domain, coronavirus / 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 ...Non-structural protein 5, gammacoronavirus / DNA2/NAM7 helicase, helicase domain / AAA domain / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / NSP15, NendoU domain, coronavirus / 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 Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface domain profile. / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Nidovirus 2-O-methyltransferase / Nidovirus 2'-O-methyltransferase (2'-O-MTase) 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 3'-5' exoribonuclease (ExoN) 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 / 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 / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Trypsin-like serine proteases / Papain-like viral protease, palm and finger domains, 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 / Thrombin, subunit H / Non-structural protein 3, X-domain-like / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain / Macro domain-like / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain
Similarity search - Domain/homology
: / Chem-B1S / Chem-K36 / ORF1ab polyprotein
Similarity search - Component
Biological speciesBeluga whale coronavirus SW1
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsShaqra, A.M. / Schiffer, C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Viruses / Year: 2023
Title: Crystal Structures of Inhibitor-Bound Main Protease from Delta- and Gamma-Coronaviruses.
Authors: Zvornicanin, S.N. / Shaqra, A.M. / Huang, Q.J. / Ornelas, E. / Moghe, M. / Knapp, M. / Moquin, S. / Dovala, D. / Schiffer, C.A. / Kurt Yilmaz, N.
History
DepositionAug 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: main protease
B: main protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,51912
Polymers67,0242
Non-polymers2,49510
Water14,304794
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-20 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.083, 84.159, 68.498
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein main protease / Mpro


Mass: 33512.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Beluga whale coronavirus SW1 / Production host: Escherichia coli (E. coli) / References: UniProt: B2BW31
#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


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 485.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N3O8S / Feature type: SUBJECT OF INVESTIGATION / References: BIRD: PRD_002495
#3: Chemical ChemComp-B1S / (1R,2S)-2-({N-[(benzyloxy)carbonyl]-L-leucyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid


Type: peptide-like / Mass: 485.551 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H31N3O8S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 794 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 10-20 % (w/v) PEG 3350, 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: Apr 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.65→12.24 Å / Num. obs: 81531 / % possible obs: 94.95 % / Redundancy: 2.4 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05568 / Rpim(I) all: 0.03864 / Rrim(I) all: 0.06827 / Net I/σ(I): 11.31
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4862 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 7698 / CC1/2: 0.735 / CC star: 0.921 / Rpim(I) all: 0.3696 / Rrim(I) all: 0.6148 / % possible all: 90.26

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Not submitted

Resolution: 1.65→12.24 Å / SU ML: 0.1589 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.3908
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.195 1999 2.45 %
Rwork0.1593 79529 -
obs0.1602 81528 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.98 Å2
Refinement stepCycle: LAST / Resolution: 1.65→12.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4566 0 94 794 5454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01744850
X-RAY DIFFRACTIONf_angle_d1.51246584
X-RAY DIFFRACTIONf_chiral_restr0.1025706
X-RAY DIFFRACTIONf_plane_restr0.0108840
X-RAY DIFFRACTIONf_dihedral_angle_d15.0661640
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.27551360.24315310X-RAY DIFFRACTION89.99
1.69-1.740.25111400.21695417X-RAY DIFFRACTION91.23
1.74-1.790.25281310.21515482X-RAY DIFFRACTION92.02
1.79-1.850.22221420.19985568X-RAY DIFFRACTION93.22
1.85-1.910.22121410.18795600X-RAY DIFFRACTION94.16
1.91-1.990.21091310.17545643X-RAY DIFFRACTION95.23
1.99-2.080.23191570.1585710X-RAY DIFFRACTION95.88
2.08-2.190.2031440.15765749X-RAY DIFFRACTION96.7
2.19-2.320.19121320.15325804X-RAY DIFFRACTION96.99
2.32-2.50.19881530.16235820X-RAY DIFFRACTION97.49
2.5-2.750.20191490.1585880X-RAY DIFFRACTION98.16
2.75-3.140.18741550.15545881X-RAY DIFFRACTION98.6
3.14-3.940.1611410.13275898X-RAY DIFFRACTION98.21
3.94-12.240.16051470.13655767X-RAY DIFFRACTION94.85

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