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Basic information

Entry
Database: PDB / ID: 5sai
TitlePanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z1424343998
ComponentsUridylate-specific endoribonuclease
KeywordsHYDROLASE/HYDROLASE inhibitor / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / nsp15 / nendoU / sars-cov-2 / sars / covid / covid19 / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy ...Maturation of replicase proteins / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Transcription of SARS-CoV-2 sgRNAs / host cell endosome / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Translation of Replicase and Assembly of the Replication Transcription Complex / 5'-3' RNA helicase activity / RNA phosphodiester bond hydrolysis, exonucleolytic / Lyases; Phosphorus-oxygen lyases / modulation by virus of host autophagy / mRNA methylation / double membrane vesicle viral factory outer membrane / suppression by virus of host translation / ISG15-specific protease activity / host cell Golgi apparatus / Replication of the SARS-CoV-2 genome / suppression by virus of host type I interferon production / host cell endoplasmic reticulum / SARS coronavirus main proteinase / induction by virus of catabolism of host mRNA / cytoplasmic viral factory / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 3'-5'-exoribonuclease activity / G-quadruplex RNA binding / host cell endoplasmic reticulum-Golgi intermediate compartment / suppression by virus of host ISG15-protein conjugation / protein K48-linked deubiquitination / suppression by virus of host toll-like receptor signaling pathway / suppression by virus of host viral-induced cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / transcription, RNA-templated / suppression by virus of host NF-kappaB cascade / viral transcription / modulation by virus of host protein ubiquitination / protein K63-linked deubiquitination / methyltransferase cap1 / positive stranded viral RNA replication / protein autoprocessing / cysteine-type peptidase activity / viral genome replication / mRNA (nucleoside-2'-O-)-methyltransferase activity / suppression by virus of host TRAF activity / helicase activity / ubiquitinyl hydrolase 1 / DNA helicase / thiol-dependent deubiquitinase / DNA helicase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / endonuclease activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / suppression by virus of host type I interferon-mediated signaling pathway / transcription, DNA-templated / host cell cytoplasm / protein dimerization activity / : / protein homodimerization activity / zinc ion binding / integral component of membrane / ATP binding / identical protein binding / cytosol
Similarity search - Function
RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. ...RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nonstructural protein 14, betacoronavirus / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) domain profile. / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Viral (Superfamily 1) RNA helicase / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP15, NendoU domain, coronavirus / Nonstructural protein 13, 1B domain, coronavirus / RNA polymerase, N-terminal, coronavirus / Coronavirus proofreading exoribonuclease / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / Non-structural protein NSP15, N-terminal domain superfamily, coronavirus / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Non-structural protein NSP15, middle domain superfamily / Coronavirus RNA-dependent RNA polymerase, N-terminal / Coronavirus 2'-O-methyltransferase / Coronavirus replicase NSP15, N-terminal oligomerisation / Coronavirus replicase NSP15, middle domain / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Sarbecovirus Nsp3c-N domain profile. / Betacoronavirus replicase NSP3, N-terminal / Non-structural protein NSP3, SUD-N (Mac2) domain superfamily, betacoronavirus / Polyprotein cleavage domain PL2pro superfamily, coronavirus / Non-structural protein NSP1 superfamily, betacoronavirus / Non-structural protein 2, SARS-CoV-like / Betacoronavirus SUD-C domain / Non-structural protein NSP3, N-terminal, betacoronavirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / NendoU domain, nidovirus / Endoribonuclease EndoU-like / Carbamoyl-phosphate synthase subdomain signature 2. / Betacoronavirus (BetaCoV) Nsp1 C-terminal domain profile. / (+) RNA virus helicase core domain / (+)RNA virus helicase core domain profile. / Betacoronavirus Nsp3c-M domain profile. / Non-structural protein NSP3, SUD-M domain, betacoronavirus / Betacoronavirus replicase NSP1 / Non-structural protein NSP3, SUD-M domain superfamily, betacoronavirus / Betacoronavirus single-stranded poly(A) binding domain / Non-structural protein NSP1, betacoronavirus / Coronavirus (CoV) Nsp1 globular domain profile. / Betacoronavirus Nsp3e nucleic acid-binding (NAB) domain profile. / Betacoronavirus Nsp3c-C domain profile. / DPUP/SUD, C-terminal, betacoronavirus / Non-structural protein 6, betacoronavirus / Replicase polyprotein, nucleic acid-binding domain superfamily / Non-structural protein NSP3, nucleic acid-binding domain, betacoronavirus / Betacoronavirus nucleic acid-binding (NAB) / Non-structural protein NSP3A domain-like superfamily / Coronavirus (CoV) ExoN/MTase coactivator domain profile. / Coronavirus Nsp9 single-stranded RNA (ssRNA)-binding domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp8 cofactor domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile. / Papain-like protease, N-terminal domain superfamily, coronavirus / Lipocalin signature. / Papain-like viral protease, palm and finger domains, coronavirus / Nonstructural protein 2, N-terminal domain, coronavirus / Coronavirus replicase NSP2, N-terminal / Coronavirus Nsp3d Ubl domain profile. / Coronavirus Nsp3a Ubl domain profile. / NSP3, first ubiquitin-like (Ubl) domain, coronavirus / Non-structural protein 2, C-terminal domain, coronavirus / Coronavirus replicase NSP2, C-terminal / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Coronavirus replicase NSP4, C-terminal / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP8 / Coronavirus replicase NSP6 / Coronavirus papain-like peptidase / Non-structural protein NSP8, coronavirus-like / Coronavirus replicase NSP4, N-terminal / Coronavirus endopeptidase C30 / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Non-structural protein 6, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / Non-structural protein NSP9, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Coronavirus replicase NSP4, N-terminal / Peptidase C16, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Peptidase C30, coronavirus / Non-structural protein NSP9 superfamily, coronavirus
Similarity search - Domain/homology
N-{2-[(propan-2-yl)sulfanyl]phenyl}urea / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / molecular replacement / Resolution: 2.022 Å
AuthorsGodoy, A.S. / Douangamath, A. / Nakamura, A.M. / Dias, A. / Krojer, T. / Noske, G.D. / Gawiljuk, V.O. / Fernandes, R.S. / Fairhead, M. / Powell, A. ...Godoy, A.S. / Douangamath, A. / Nakamura, A.M. / Dias, A. / Krojer, T. / Noske, G.D. / Gawiljuk, V.O. / Fernandes, R.S. / Fairhead, M. / Powell, A. / Dunnet, L. / Aimon, A. / Fearon, D. / Brandao-Neto, J. / Skyner, R. / von Delft, F. / Oliva, G.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Fundacao de Amparo a Pesquisa do Estado de Sao Paulo2013/07600-3 Brazil
CitationJournal: To Be Published
Title: PanDDA analysis group deposition
Authors: Godoy, A.S. / Douangamath, A. / Nakamura, A.M. / Dias, A. / Krojer, T. / Noske, G.D. / Gawiljuk, V.O. / Fernandes, R.S. / Fairhead, M. / Powell, A. / Dunnet, L. / Aimon, A. / Fearon, D. / ...Authors: Godoy, A.S. / Douangamath, A. / Nakamura, A.M. / Dias, A. / Krojer, T. / Noske, G.D. / Gawiljuk, V.O. / Fernandes, R.S. / Fairhead, M. / Powell, A. / Dunnet, L. / Aimon, A. / Fearon, D. / Brandao-Neto, J. / Skyner, R. / von Delft, F. / Oliva, G.
History
DepositionMay 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4353
Polymers78,2252
Non-polymers2101
Water12,917717
1
A: Uridylate-specific endoribonuclease

A: Uridylate-specific endoribonuclease

A: Uridylate-specific endoribonuclease

B: Uridylate-specific endoribonuclease
hetero molecules

B: Uridylate-specific endoribonuclease
hetero molecules

B: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)235,3069
Polymers234,6756
Non-polymers6313
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation4_545-x,-y-1,z+1/21
crystal symmetry operation5_555y,-x+y,z+1/21
crystal symmetry operation6_445x-y-1,x-1,z+1/21
Buried area19330 Å2
ΔGint-114 kcal/mol
Surface area82660 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)149.947, 149.947, 112.860
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Uridylate-specific endoribonuclease / NendoU / Non-structural protein 15 / nsp15


Mass: 39112.535 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 (E. coli)
References: UniProt: P0DTD1, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ZQM / N-{2-[(propan-2-yl)sulfanyl]phenyl}urea


Mass: 210.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N2OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 717 / 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: 4.68 Å3/Da / Density % sol: 73.73 % / Mosaicity: 0 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Na3 Citrate pH 5,14% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91266 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91266 Å / Relative weight: 1
ReflectionResolution: 2.02→129.85 Å / Num. obs: 94026 / % possible obs: 99.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 36.96 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.272 / Rpim(I) all: 0.09 / Rrim(I) all: 0.287 / Net I/σ(I): 6 / Num. measured all: 949707 / Scaling rejects: 2892
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.02-2.0610.23.3344652245480.4071.0933.5110.897.8
11.07-129.8510.60.04465066110.9990.0160.04728.9100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3 (18-SEP-2020)refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.23data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6X1B
Resolution: 2.022→129.86 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.896 / SU R Cruickshank DPI: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.127 / SU Rfree Cruickshank DPI: 0.124
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4244 4.92 %RANDOM
Rwork0.1952 ---
obs0.1965 86272 91.7 %-
Displacement parametersBiso max: 103.65 Å2 / Biso mean: 47.29 Å2 / Biso min: 16.97 Å2
Baniso -1Baniso -2Baniso -3
1-9.6943 Å20 Å20 Å2
2--9.6943 Å20 Å2
3----19.3886 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: final / Resolution: 2.022→129.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5500 0 14 717 6231
Biso mean--99.26 50.84 -
Num. residues----696
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1957SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes960HARMONIC5
X-RAY DIFFRACTIONt_it5646HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion742SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5293SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5646HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg7662HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion17.45
LS refinement shellResolution: 2.02→2.05 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2354 64 3.71 %
Rwork0.2277 1662 -
all-1726 -
obs--47.59 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.70990.2291-0.15010.82770.16570.484-0.02970.0932-0.0014-0.03990.0661-0.2254-0.0085-0.059-0.0364-0.0314-0.03150.02070.00820.0266-0.095521.4251-83.704211.862
20.62620.2778-0.06340.9915-0.54710.57360.1139-0.0549-0.01170.0516-0.03930.2742-0.06920.0474-0.0746-0.0768-0.01610.04-0.0499-0.02160.012454.5785-50.82933.2157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A-1 - 346
2X-RAY DIFFRACTION2{ B|* }B-1 - 346

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