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- PDB-5r81: PanDDA analysis group deposition -- Crystal Structure of COVID-19... -

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Basic information

Entry
Database: PDB / ID: 5r81
TitlePanDDA analysis group deposition -- Crystal Structure of COVID-19 main protease in complex with Z1367324110
Components3C-like proteinase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


modulation by virus of host autophagy / mRNA methylation / RNA phosphodiester bond hydrolysis, exonucleolytic / suppression by virus of host translation / ISG15-specific protease activity / suppression by virus of host type I interferon production / suppression by virus of host toll-like receptor signaling pathway / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory ...modulation by virus of host autophagy / mRNA methylation / RNA phosphodiester bond hydrolysis, exonucleolytic / suppression by virus of host translation / ISG15-specific protease activity / suppression by virus of host type I interferon production / suppression by virus of host toll-like receptor signaling pathway / induction by virus of catabolism of host mRNA / SARS coronavirus main proteinase / cytoplasmic viral factory / suppression by virus of host ISG15 activity / protein K48-linked deubiquitination / 3'-5'-exoribonuclease activity / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / exonuclease activity / suppression by virus of host IRF3 activity / modulation by virus of host protein ubiquitination / suppression by virus of host NF-kappaB transcription factor activity / transcription, RNA-templated / protein K63-linked deubiquitination / viral genome replication / positive stranded viral RNA replication / protein autoprocessing / Transferases; Transferring one-carbon groups; Methyltransferases / suppression by virus of host TRAF activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / viral transcription / host cell membrane / helicase activity / ubiquitinyl hydrolase 1 / cysteine-type peptidase activity / DNA helicase / methyltransferase activity / DNA helicase activity / single-stranded RNA binding / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / thiol-dependent deubiquitinase / host cell perinuclear region of cytoplasm / viral protein processing / methylation / RNA helicase / induction by virus of host autophagy / suppression by virus of host type I interferon-mediated signaling pathway / RNA-directed RNA polymerase / endonuclease activity / cysteine-type endopeptidase activity / RNA-directed 5'-3' RNA polymerase activity / viral RNA genome replication / RNA helicase activity / transcription, DNA-templated / host cell cytoplasm / Hydrolases; Acting on ester bonds / protein dimerization activity / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding
Macro domain / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP8 superfamily, coronavirus / Endoribonuclease EndoU-like / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Non-structural protein NSP4, C-terminal, coronavirus / S-adenosyl-L-methionine-dependent methyltransferase ...Macro domain / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Non-structural protein NSP8 superfamily, coronavirus / Endoribonuclease EndoU-like / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP3, nucleic acid-binding (NAR) domain, betacoronavirus / Non-structural protein NSP4, C-terminal, coronavirus / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / (+) RNA virus helicase core domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Non-structural protein NSP3A domain-like superfamily / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein NSP1, betacoronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP8, coronavirus-like / Non-structural protein NSP7, coronavirus / Non-structural protein NSP9, coronavirus / Peptidase C16, coronavirus / RNA polymerase, N-terminal, coronaviral / Non-structural protein 14, coronavirus / Non-structural protein NSP16, coronavirus-like / Peptidase S1, PA clan / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / RNA-directed RNA polymerase, C-terminal domain / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Non-structural protein 6, coronavirus / NendoU domain, nidovirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Peptidase S1, PA clan, chymotrypsin-like fold / Papain-like viral protease, palm and finger domains, coronavirus / DNA/RNA polymerase superfamily / Non-structural protein NSP3, SUD-N (Mac2) domain, betacoronavirus / Peptidase C30, domain 3, coronavirus / Yro2-like, 7TM domain / Macro domain-like / Papain-like protease, thumb domain superfamily, coronavirus / Papain-like protease, N-terminal domain superfamily, coronavirus / Non-structural protein NSP15, middle domain superfamily / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / DNA2/NAM7 helicase-like, C-terminal / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Peptidase C30, coronavirus / main proteinase (3clpro) structure, domain 3 / main proteinase (3clpro) structure, domain 3 / Trypsin-like serine proteases / Thrombin, subunit H / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Replicase polyprotein 1ab
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 1.95 Å
AuthorsFearon, D. / Powell, A.J. / Douangamath, A. / Owen, C.D. / Wild, C. / Krojer, T. / Lukacik, P. / Strain-Damerell, C.M. / Walsh, M.A. / von Delft, F.
CitationJournal: Nat Commun / Year: 2020
Title: Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
Authors: Douangamath, A. / Fearon, D. / Gehrtz, P. / Krojer, T. / Lukacik, P. / Owen, C.D. / Resnick, E. / Strain-Damerell, C. / Aimon, A. / Abranyi-Balogh, P. / Brandao-Neto, J. / Carbery, A. / ...Authors: Douangamath, A. / Fearon, D. / Gehrtz, P. / Krojer, T. / Lukacik, P. / Owen, C.D. / Resnick, E. / Strain-Damerell, C. / Aimon, A. / Abranyi-Balogh, P. / Brandao-Neto, J. / Carbery, A. / Davison, G. / Dias, A. / Downes, T.D. / Dunnett, L. / Fairhead, M. / Firth, J.D. / Jones, S.P. / Keeley, A. / Keseru, G.M. / Klein, H.F. / Martin, M.P. / Noble, M.E.M. / O'Brien, P. / Powell, A. / Reddi, R.N. / Skyner, R. / Snee, M. / Waring, M.J. / Wild, C. / London, N. / von Delft, F. / Walsh, M.A.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Structure summary / Category: entity / struct / Item: _entity.pdbx_description / _struct.pdbx_descriptor
Revision 1.2May 6, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_related_exp_data_set / struct_ref / struct_ref_seq
Item: _entity.pdbx_description / _entity.pdbx_ec ..._entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_gene / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession
Revision 1.3Jan 27, 2021Group: Structure summary / Category: entity / entity_name_com / Item: _entity.pdbx_ec / _entity_name_com.name
Revision 1.4Feb 24, 2021Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3646
Polymers33,8261
Non-polymers5395
Water6,017334
1
A: 3C-like proteinase
hetero molecules

A: 3C-like proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,72912
Polymers67,6512
Non-polymers1,07810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4650 Å2
ΔGint-0 kcal/mol
Surface area25280 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)113.780, 53.490, 44.450
Angle α, β, γ (deg.)90.000, 101.700, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1338-

HOH

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Components

#1: Protein 3C-like proteinase / SARS-CoV-2 main protease / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 ...SARS-CoV-2 main protease / 3CL-PRO / 3CLp / Main protease / Mpro / Non-structural protein 5 / nsp5 / SARS coronavirus main proteinase


Mass: 33825.547 Da / Num. of mol.: 1
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 (E. coli)
References: UniProt: P0DTD1, SARS coronavirus main proteinase
#2: Chemical ChemComp-RZJ / 1-methyl-3,4-dihydro-2~{H}-quinoline-7-sulfonamide


Mass: 226.295 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 1.96 Å3/Da / Density % sol: 37.18 % / Mosaicity: 0 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 4K, 5% DMSO / PH range: 0.1M

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9126 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9126 Å / Relative weight: 1
ReflectionResolution: 1.84→55.68 Å / Num. obs: 22778 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.979 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.097 / Rrim(I) all: 0.189 / Net I/σ(I): 4 / Num. measured all: 83978 / Scaling rejects: 176
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.881.582519113570.3040.921.8370.799.8
9.01-55.680.1218072100.9670.070.1410.599.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6LU7
Resolution: 1.95→48.27 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.422 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.388 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 985 5.1 %RANDOM
Rwork0.182 ---
Obs0.1854 18207 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 179.18 Å2 / Biso mean: 44.601 Å2 / Biso min: 24.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å21 Å2
2---1.33 Å20 Å2
3---0.04 Å2
Refinement stepCycle: final / Resolution: 1.95→48.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 31 334 2712
Biso mean--95.61 51.6 -
Num. residues----304
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0143463
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172480
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.6553792
X-RAY DIFFRACTIONr_angle_other_deg1.3041.5825767
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9715360
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34924.088137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8815439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5291511
X-RAY DIFFRACTIONr_chiral_restr0.0670.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023201
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
X-RAY DIFFRACTIONr_mcbond_it2.4234.6421944
X-RAY DIFFRACTIONr_mcbond_other2.7794.2671475
X-RAY DIFFRACTIONr_mcangle_it4.1516.3211760
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 60 -
Rwork0.378 1347 -
All-1407 -
Obs--99.65 %

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