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- PDB-7k9p: Room temperature structure of NSP15 Endoribonuclease from SARS Co... -

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Basic information

Entry
Database: PDB / ID: 7k9p
TitleRoom temperature structure of NSP15 Endoribonuclease from SARS CoV-2 solved using SFX.
ComponentsUridylate-specific endoribonuclease
KeywordsVIRAL PROTEIN / Severe acute respiratory syndrome coronavirus 2 / room temperature structure / serial femtosecond crystallography
Function / homology
Function and homology information


protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / TRAF3-dependent IRF activation pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / 5'-3' DNA helicase activity / symbiont-mediated suppression of host NF-kappaB cascade / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / ubiquitinyl hydrolase 1 / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / host cell perinuclear region of cytoplasm / viral protein processing / host cell endoplasmic reticulum membrane / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / 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
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 / : ...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 Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Coronavirus Nsp12 Interface 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 / Nidovirus 2-O-methyltransferase / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Non-structural protein NSP16, coronavirus-like / Non-structural protein 14, coronavirus / RNA polymerase, N-terminal, coronavirus / Nidovirus 3'-5' exoribonuclease domain / Coronavirus 2'-O-methyltransferase / Coronavirus proofreading exoribonuclease / Coronavirus RNA-dependent RNA polymerase, N-terminal / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / 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 / 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 / NSP1, globular domain, alpha/betacoronavirus / Coronavirus (CoV) Nsp2 middle domain profile. / 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 / : / : / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Coronavirus 3Ecto domain profile. / Coronavirus RNA-dependent RNA polymerase (RdRp) Nsp7 cofactor domain profile.
Similarity search - Domain/homology
CITRIC ACID / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBotha, S. / Jernigan, R. / Chen, J. / Coleman, M.A. / Frank, M. / Grant, T.D. / Hansen, D.T. / Ketawala, G. / Logeswaran, D. / Martin-Garcia, J. ...Botha, S. / Jernigan, R. / Chen, J. / Coleman, M.A. / Frank, M. / Grant, T.D. / Hansen, D.T. / Ketawala, G. / Logeswaran, D. / Martin-Garcia, J. / Nagaratnam, N. / Raj, A.L.L.X. / Shelby, M. / Yang, J.-H. / Yung, M.C. / Fromme, P.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)NSF2031343 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095583 United States
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: Structure / Year: 2022
Title: Room-temperature structural studies of SARS-CoV-2 protein NendoU with an X-ray free-electron laser.
Authors: Jernigan, R.J. / Logeswaran, D. / Doppler, D. / Nagaratnam, N. / Sonker, M. / Yang, J.H. / Ketawala, G. / Martin-Garcia, J.M. / Shelby, M.L. / Grant, T.D. / Mariani, V. / Tolstikova, A. / ...Authors: Jernigan, R.J. / Logeswaran, D. / Doppler, D. / Nagaratnam, N. / Sonker, M. / Yang, J.H. / Ketawala, G. / Martin-Garcia, J.M. / Shelby, M.L. / Grant, T.D. / Mariani, V. / Tolstikova, A. / Sheikh, M.Z. / Yung, M.C. / Coleman, M.A. / Zaare, S. / Kaschner, E.K. / Rabbani, M.T. / Nazari, R. / Zacks, M.A. / Hayes, B. / Sierra, R.G. / Hunter, M.S. / Lisova, S. / Batyuk, A. / Kupitz, C. / Boutet, S. / Hansen, D.T. / Kirian, R.A. / Schmidt, M. / Fromme, R. / Frank, M. / Ros, A. / Chen, J.J. / Botha, S. / Fromme, P.
History
DepositionSep 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 25, 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: Uridylate-specific endoribonuclease
B: Uridylate-specific endoribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7434
Polymers78,3592
Non-polymers3842
Water28816
1
A: Uridylate-specific endoribonuclease
hetero molecules

A: Uridylate-specific endoribonuclease
hetero molecules

A: Uridylate-specific endoribonuclease
hetero molecules

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)236,23012
Polymers235,0786
Non-polymers1,1536
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_445-x-1,-y-1,z+1/21
crystal symmetry operation5_545y,-x+y-1,z+1/21
crystal symmetry operation6_555x-y,x,z+1/21
Buried area18760 Å2
ΔGint-119 kcal/mol
Surface area89850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.000, 154.000, 117.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 39179.605 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) / Strain (production host): BL21-Gold (DE3)
References: UniProt: P0DTD1, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 25066

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Sample preparation

CrystalDensity Matthews: 5.11 Å3/Da / Density % sol: 75.93 %
Crystal growTemperature: 295 K / Method: batch mode / pH: 5.5
Details: NendoU protein 75 mg/ml (20 mM HEPES pH 7.5, 150mM NaCl, 1mM TCEP) is added to the precipitant solution (100mM Na Citrate pH 5.5, 20% PEG 1000, 20% 2-Methyl-2,4-pentanediol (MPD)) in a 1:7 ...Details: NendoU protein 75 mg/ml (20 mM HEPES pH 7.5, 150mM NaCl, 1mM TCEP) is added to the precipitant solution (100mM Na Citrate pH 5.5, 20% PEG 1000, 20% 2-Methyl-2,4-pentanediol (MPD)) in a 1:7 protein:precipitant ratio with agitation at 295K overnight.

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Data collection

DiffractionMean temperature: 295 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: MFX / Wavelength: 1.277 Å
DetectorType: SLAC ePix10k 2M / Detector: PIXEL / Date: Sep 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.277 Å / Relative weight: 1
ReflectionResolution: 2.6→33.67 Å / Num. obs: 48524 / % possible obs: 100 % / Redundancy: 101 % / CC1/2: 0.94 / CC star: 0.98 / Net I/σ(I): 3.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 70 % / Mean I/σ(I) obs: 0.2 / Num. unique obs: 4435 / CC1/2: 0.03 / CC star: 0.23 / % possible all: 100
Serial crystallography measurementPulse duration: 30 fsec. / XFEL pulse repetition rate: 120 Hz
Serial crystallography sample deliveryMethod: injection
Serial crystallography sample delivery injectionDescription: MESH injector
Serial crystallography data reductionCrystal hits: 25066 / Lattices indexed: 25066

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystFEL0.9.1data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6xdh

6xdh


Resolution: 2.6→33.67 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.932 / SU B: 6.183 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20877 2503 5.2 %RANDOM
Rwork0.19137 ---
obs0.19229 45981 99.9 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.684 Å2
Baniso -1Baniso -2Baniso -3
1--8.54 Å2-0 Å2-0 Å2
2---8.54 Å2-0 Å2
3---17.07 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5504 0 26 16 5546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195644
X-RAY DIFFRACTIONr_bond_other_d0.0010.025243
X-RAY DIFFRACTIONr_angle_refined_deg1.0341.8847657
X-RAY DIFFRACTIONr_angle_other_deg0.9092.93412202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3475694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2625.331257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78515980
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6571518
X-RAY DIFFRACTIONr_chiral_restr0.060.2873
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026238
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021100
X-RAY DIFFRACTIONr_mcbond_it0.4584.0212782
X-RAY DIFFRACTIONr_mcbond_other0.4584.022781
X-RAY DIFFRACTIONr_mcangle_it0.8296.0283474
X-RAY DIFFRACTIONr_mcangle_other0.8296.0293475
X-RAY DIFFRACTIONr_scbond_it0.2674.0792862
X-RAY DIFFRACTIONr_scbond_other0.2664.0772859
X-RAY DIFFRACTIONr_scangle_other0.5026.0984184
X-RAY DIFFRACTIONr_long_range_B_refined1.27844.8675629
X-RAY DIFFRACTIONr_long_range_B_other1.27844.8725630
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 191 -
Rwork0.283 3372 -
obs--99.78 %
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)
10.5353-0.084-0.03670.5634-0.12350.44550.01070.11570.0921-0.109-0.012-0.0003-0.04750.00790.00130.1485-0.0039-0.03260.15550.00320.0741-13.883-71.2054.985
20.63370.1850.27850.51230.08010.4829-0.0163-0.0946-0.03940.05930.003-0.05540.03220.00070.01330.12640.00630.01510.12990.0220.0626-59.41-58.456-5.083

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