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- PDB-7ene: Crystal structure of MERS-CoV 3CLpro in complex with the non-cova... -

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Entry
Database: PDB / ID: 7ene
TitleCrystal structure of MERS-CoV 3CLpro in complex with the non-covalent inhibitor WU-04
ComponentsORF1a protein
KeywordsVIRAL PROTEIN / Non-covalent / Inhibitor / 3CLpro / Coronavirus
Function / homology
Function and homology information


host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity ...host cell membrane / viral genome replication / methyltransferase activity / symbiont-mediated degradation of host mRNA / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / methylation / symbiont-mediated perturbation of host ubiquitin-like protein modification / cysteine-type deubiquitinase activity / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / zinc ion binding / membrane
Similarity search - Function
Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 ...Non-structural protein 2, MERS-CoV-like / NSP3, SUD-C domain, MERS-CoV-like / : / Betacoronavirus Nsp3e group 2-specific marker (G2M) domain profile. / NSP1, C-terminal domain, betacoronavirus / Betacoronavirus Nsp3c-M domain profile. / NSP1, globular domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus replicase NSP1 / Betacoronavirus single-stranded poly(A) binding domain / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3c-C domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Papain-like protease, N-terminal domain superfamily, coronavirus / Papain-like viral protease, palm and finger domains, coronavirus / : / Coronavirus 3Ecto domain profile. / : / 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 / 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-J7R / 1A polyprotein
Similarity search - Component
Biological speciesMiddle East respiratory syndrome coronavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsHou, N. / Peng, C. / Hu, Q.
CitationJournal: Acs Cent.Sci. / Year: 2023
Title: Development of Highly Potent Noncovalent Inhibitors of SARS-CoV-2 3CLpro.
Authors: Hou, N. / Shuai, L. / Zhang, L. / Xie, X. / Tang, K. / Zhu, Y. / Yu, Y. / Zhang, W. / Tan, Q. / Zhong, G. / Wen, Z. / Wang, C. / He, X. / Huo, H. / Gao, H. / Xu, Y. / Xue, J. / Peng, C. / ...Authors: Hou, N. / Shuai, L. / Zhang, L. / Xie, X. / Tang, K. / Zhu, Y. / Yu, Y. / Zhang, W. / Tan, Q. / Zhong, G. / Wen, Z. / Wang, C. / He, X. / Huo, H. / Gao, H. / Xu, Y. / Xue, J. / Peng, C. / Zou, J. / Schindewolf, C. / Menachery, V. / Su, W. / Yuan, Y. / Shen, Z. / Zhang, R. / Yuan, S. / Yu, H. / Shi, P.Y. / Bu, Z. / Huang, J. / Hu, Q.
History
DepositionApr 16, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.3Nov 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 protein
B: ORF1a protein
C: ORF1a protein
D: ORF1a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,5228
Polymers133,4174
Non-polymers2,1064
Water00
1
A: ORF1a protein
B: ORF1a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7614
Polymers66,7082
Non-polymers1,0532
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-19 kcal/mol
Surface area24710 Å2
MethodPISA
2
C: ORF1a protein
D: ORF1a protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7614
Polymers66,7082
Non-polymers1,0532
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-18 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.755, 112.952, 92.355
Angle α, β, γ (deg.)90.000, 91.316, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
ORF1a protein


Mass: 33354.172 Da / Num. of mol.: 4 / Fragment: UNP residues 3248-3553
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Middle East respiratory syndrome coronavirus
Gene: orf1ab / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7E693
#2: Chemical
ChemComp-J7R / ~{N}-[(1~{S},2~{R})-2-[[4-bromanyl-2-(methylcarbamoyl)-6-nitro-phenyl]amino]cyclohexyl]isoquinoline-4-carboxamide


Mass: 526.382 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H24BrN5O4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.45 Å3/Da / Density % sol: 49.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 4% v/v Tacsimate pH 5.0, 0.1M sodium citrate tribasic pH 5.4, 12% v/v PEG 3,350, 8 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.541 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Jan 21, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.98→29.18 Å / Num. obs: 25971 / % possible obs: 98.42 % / Redundancy: 4.8 % / Biso Wilson estimate: 36.42 Å2 / CC1/2: 0.947 / Rpim(I) all: 0.1235 / Rrim(I) all: 0.2769 / Net I/σ(I): 10.58
Reflection shellResolution: 2.98→3.086 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.72 / Num. unique obs: 2568 / CC1/2: 0.866 / Rpim(I) all: 0.2094 / Rrim(I) all: 0.4803 / % possible all: 99.38

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Processing

Software
NameVersionClassification
CrysalisPro1.171.40.73adata collection
PHENIX1.17.1_3660refinement
CrysalisPro1.171.40.73adata reduction
CrysalisPro1.171.40.73adata scaling
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ylu

4ylu


Resolution: 2.98→29.18 Å / SU ML: 0.3898 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.6291
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2745 1182 4.55 %
Rwork0.2349 24777 -
obs0.2367 25959 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.32 Å2
Refinement stepCycle: LAST / Resolution: 2.98→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9248 0 136 0 9384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00559612
X-RAY DIFFRACTIONf_angle_d1.01613092
X-RAY DIFFRACTIONf_chiral_restr0.05841484
X-RAY DIFFRACTIONf_plane_restr0.00611664
X-RAY DIFFRACTIONf_dihedral_angle_d16.99413320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.98-3.120.36141470.30343073X-RAY DIFFRACTION99.35
3.12-3.280.37541540.30243113X-RAY DIFFRACTION99.15
3.28-3.480.33121420.28213116X-RAY DIFFRACTION99.24
3.48-3.750.28241510.25833087X-RAY DIFFRACTION98.87
3.75-4.130.30661440.2383076X-RAY DIFFRACTION98.35
4.13-4.720.24351500.20323105X-RAY DIFFRACTION98.46
4.73-5.950.21681500.20043115X-RAY DIFFRACTION98.61
5.95-29.180.20341440.17733092X-RAY DIFFRACTION96.28
Refinement TLS params.Method: refined / Origin x: 25.6357041015 Å / Origin y: -25.978363762 Å / Origin z: 69.0568660854 Å
111213212223313233
T0.0948121366754 Å2-0.0657299839582 Å20.0347361883533 Å2-0.139172949936 Å20.00541385707454 Å2--0.148226788028 Å2
L0.267354162663 °2-0.210980795746 °20.243294714112 °2-0.316156067835 °2-0.225877908558 °2--1.31567228853 °2
S-0.0213126079689 Å °0.0513978185782 Å °-0.0106199766638 Å °0.0699056559514 Å °0.000491459764364 Å °0.00991471181918 Å °-0.102037634472 Å °0.146148629845 Å °0.00263475646521 Å °
Refinement TLS groupSelection details: all

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