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- PDB-7qt8: Room temperature In-situ SARS-CoV-2 MPRO with bound ABT-957 -

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Basic information

Entry
Database: PDB / ID: 7qt8
TitleRoom temperature In-situ SARS-CoV-2 MPRO with bound ABT-957
Components3C-like proteinase
KeywordsVIRAL PROTEIN / Protease / Dimer / Main protease / SARS-CoV-2
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity ...protein guanylyltransferase activity / RNA endonuclease activity producing 3'-phosphomonoesters, hydrolytic mechanism / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Maturation of replicase proteins / TRAF3-dependent IRF activation pathway / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / snRNP Assembly / Replication of the SARS-CoV-2 genome / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / host cell endosome / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated suppression of host NF-kappaB cascade / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / copper ion binding / viral translational frameshifting / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. ...main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-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 / : / Lipocalin signature. / DNA2/NAM7 helicase-like, C-terminal / AAA domain / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Sarbecovirus Nsp3c-N domain profile. / Non-structural protein NSP3, N-terminal, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, betacoronavirus / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Betacoronavirus SUD-C domain / Betacoronavirus replicase NSP3, N-terminal / NSP1 globular domain superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Trypsin-like serine proteases / Carbamoyl-phosphate synthase subdomain signature 2. / 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 / NSP1, C-terminal domain, betacoronavirus / : / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / Betacoronavirus Nsp3e group 2-specific marker (G2M) 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, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / Non-structural protein NSP3, nucleic acid-binding domain superfamily, betacoronavirus / Non-structural protein 6, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Papain-like viral protease, palm and finger domains, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP2, N-terminal / : / Coronavirus replicase NSP2, C-terminal / Coronavirus (CoV) Nsp2 middle domain profile. / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Coronavirus (CoV) Nsp2 N-terminal domain profile. / Coronavirus (CoV) Nsp2 C-terminal domain profile. / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, 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 / Peptidase family C16 domain profile. / : / :
Similarity search - Domain/homology
Chem-R8H / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHorrell, S. / Gildae, R.J. / Axford, D. / Owen, C.D. / Lukacik, P. / Strain-Damerell, C. / Owen, R.L. / Walsh, M.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Science and Technology Funding Council United Kingdom
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: xia2.multiplex: a multi-crystal data-analysis pipeline.
Authors: Gildea, R.J. / Beilsten-Edmands, J. / Axford, D. / Horrell, S. / Aller, P. / Sandy, J. / Sanchez-Weatherby, J. / Owen, C.D. / Lukacik, P. / Strain-Damerell, C. / Owen, R.L. / Walsh, M.A. / Winter, G.
History
DepositionJan 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 9, 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

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
B: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6244
Polymers67,6512
Non-polymers9732
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-14 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.245, 54.673, 116.578
Angle α, β, γ (deg.)90.000, 100.385, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 1 - 305 / Label seq-ID: 1 - 305

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein 3C-like proteinase / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2
Gene: rep, 1a-1b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-R8H / (2~{R})-5-oxidanylidene-~{N}-[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(pyridin-2-ylmethylamino)butan-2-yl]-1-(phenylmethyl)pyrrolidine-2-carboxamide


Mass: 486.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30N4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.1 Å3/Da / Density % sol: 41.33 % / Description: Thin Plates
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5 / Details: 11% (v/v) PEG 4K, 5% (v/v) DMSO, 0.1 M MES pH 6.5

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→49.37 Å / Num. obs: 37088 / % possible obs: 95.2 % / Redundancy: 7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.067 / Rrim(I) all: 0.184 / Net I/σ(I): 9.9
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 7 % / Rmerge(I) obs: 1.956 / Num. unique obs: 1277 / CC1/2: 0.425 / Rpim(I) all: 0.767 / Rrim(I) all: 2.11 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AEH

7aeh


Resolution: 2.01→49.37 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 15.301 / SU ML: 0.178 / Cross valid method: FREE R-VALUE / ESU R: 0.232 / ESU R Free: 0.18
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2365 1804 4.864 %
Rwork0.2037 35284 -
all0.205 --
obs-37088 98.644 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.315 Å2
Baniso -1Baniso -2Baniso -3
1-1.078 Å20 Å2-0.581 Å2
2--0.342 Å2-0 Å2
3----1.132 Å2
Refinement stepCycle: LAST / Resolution: 2.01→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4695 0 72 48 4815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134944
X-RAY DIFFRACTIONr_bond_other_d0.0020.0154553
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.6376731
X-RAY DIFFRACTIONr_angle_other_deg1.3851.57510464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8665624
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30223.195241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.92415775
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg12.095152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.1271519
X-RAY DIFFRACTIONr_chiral_restr0.1180.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025751
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021185
X-RAY DIFFRACTIONr_nbd_refined0.2070.2782
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.24131
X-RAY DIFFRACTIONr_nbtor_refined0.170.22446
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.22417
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.296
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2360.218
X-RAY DIFFRACTIONr_nbd_other0.2490.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1030.24
X-RAY DIFFRACTIONr_mcbond_it0.9671.6652475
X-RAY DIFFRACTIONr_mcbond_other0.9671.6642474
X-RAY DIFFRACTIONr_mcangle_it1.6392.4923103
X-RAY DIFFRACTIONr_mcangle_other1.6392.4933104
X-RAY DIFFRACTIONr_scbond_it1.3521.8632469
X-RAY DIFFRACTIONr_scbond_other1.3521.8632470
X-RAY DIFFRACTIONr_scangle_it2.2832.7243627
X-RAY DIFFRACTIONr_scangle_other2.2822.7243628
X-RAY DIFFRACTIONr_lrange_it3.50719.2375094
X-RAY DIFFRACTIONr_lrange_other3.50219.2265093
X-RAY DIFFRACTIONr_ncsr_local_group_10.0760.059482
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.076470.05009
12BX-RAY DIFFRACTIONLocal ncs0.076470.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.0620.3691380.3792602X-RAY DIFFRACTION98.917
2.062-2.1190.3231260.3432544X-RAY DIFFRACTION99.7013
2.119-2.180.3011450.3122451X-RAY DIFFRACTION99.6163
2.18-2.2470.331200.2862415X-RAY DIFFRACTION99.4118
2.247-2.3210.2941150.2592326X-RAY DIFFRACTION99.268
2.321-2.4020.316980.2592279X-RAY DIFFRACTION99.2899
2.402-2.4930.2671110.2442191X-RAY DIFFRACTION99.3526
2.493-2.5950.31910.2382089X-RAY DIFFRACTION99.3166
2.595-2.710.2511150.2292010X-RAY DIFFRACTION98.9292
2.71-2.8420.221870.2171928X-RAY DIFFRACTION98.2927
2.842-2.9960.243880.1971810X-RAY DIFFRACTION98.6487
2.996-3.1770.2381010.1761702X-RAY DIFFRACTION98.3633
3.177-3.3960.22880.1741628X-RAY DIFFRACTION98.2818
3.396-3.6680.218870.1651484X-RAY DIFFRACTION97.699
3.668-4.0180.156660.1411394X-RAY DIFFRACTION97.9866
4.018-4.4920.191560.1361266X-RAY DIFFRACTION97.4208
4.492-5.1850.156520.131106X-RAY DIFFRACTION97.6391
5.185-6.3470.204550.159930X-RAY DIFFRACTION96.0976
6.347-8.9630.223460.161730X-RAY DIFFRACTION96.0396
8.963-44.420.142190.154399X-RAY DIFFRACTION92.2737
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.3048-1.44020.2522.2801-0.05741.86420.06610.2174-0.02-0.1092-0.0512-0.0047-0.07680.0542-0.01490.03490.03720.0220.1042-0.0150.101815.8452-0.641615.9601
23.13220.97971.11491.98890.29732.2521-0.0228-0.0569-0.03410.01680.01510.0219-0.12980.06060.00780.01430.00010.02250.01630.01480.095319.996-0.255541.9034
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 305
2X-RAY DIFFRACTION2ALLB1 - 305

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