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- PDB-1uw7: Nsp9 protein from SARS-coronavirus. -

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Basic information

Entry
Database: PDB / ID: 1uw7
TitleNsp9 protein from SARS-coronavirus.
ComponentsNSP9
KeywordsVIRAL PROTEIN / VIRUS / REPLICASE PROTEIN / SARS / CORONAVIRUS / RNA-BINDING
Function / homology
Function and homology information


viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex ...viral RNA-directed RNA polymerase complex / exoribonuclease complex / viral replication complex formation and maintenance / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / endopeptidase complex / endoribonuclease complex / mRNA capping enzyme complex / suppression by virus of host type I interferon production / positive regulation of RNA biosynthetic process / positive stranded viral RNA replication / protein K48-linked deubiquitination / : / : / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K63-linked deubiquitination / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / RNA-templated transcription / SARS-CoV-1 modulates host translation machinery / 7-methylguanosine mRNA capping / viral transcription / protein autoprocessing / positive regulation of viral genome replication / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / helicase activity / protein processing / SARS-CoV-1 activates/modulates innate immune responses / double-stranded RNA binding / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / ISG15-specific peptidase activity / double membrane vesicle viral factory outer membrane / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / : / host cell endoplasmic reticulum-Golgi intermediate compartment / 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 / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / host cell Golgi apparatus / symbiont-mediated perturbation of host ubiquitin-like protein modification / mRNA (nucleoside-2'-O-)-methyltransferase activity / endonuclease activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / DNA helicase / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / host cell cytoplasm / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / single-stranded RNA binding / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / protein dimerization activity / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
Replicase NSP9 / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain ...Replicase NSP9 / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : / Coronavirus Nonstructural protein 13, 1B domain / Coronavirus Non-structural protein 13, zinc-binding domain / Coronavirus Nonstructural protein 13, stalk domain / : / Coronavirus Nsp12 Interface domain profile. / Nonstructural protein 15, middle domain, alpha/betacoronavirus / Nonstructural protein 15, N-terminal domain, alpha/beta-coronavirus / NSP14, guanine-N7-methyltransferase domain, coronavirus / NSP12 RNA-dependent RNA polymerase, coronavirus / Coronavirus (CoV) guanine-N7-methyltransferase (N7-MTase) domain profile. / Coronavirus (CoV) Nsp15 N-terminal oligomerization domain profile. / Nidovirus 2-O-methyltransferase / Coronavirus Nsp12 RNA-dependent RNA polymerase (RdRp) domain profile. / Nidovirus 3'-5' exoribonuclease domain / Nidovirus 2'-O-methyltransferase (2'-O-MTase) domain profile. / Nidovirus 3'-5' exoribonuclease (ExoN) domain profile. / Nonstructural protein 13, 1B domain, coronavirus / Arterivirus Nsp11 N-terminal/Coronavirus NSP15 middle domain / 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 / Coronavirus replicase NSP15, middle domain / Coronavirus replicase NSP15, N-terminal oligomerisation / Arterivirus Nsp11 N-terminal/coronavirus NSP15 middle (AV-Nsp11N/CoV-Nsp15M) 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 / Nidoviral uridylate-specific endoribonuclease (NendoU) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain / Nonstructural protein 13, zinc-binding domain, coronavirus-like / Coronaviridae zinc-binding (CV ZBD) domain profile. / Nidovirus RdRp-associated nucleotidyl transferase (NiRAN) domain profile. / Endoribonuclease EndoU-like / NendoU domain, nidovirus / Coronavirus replicase NSP15, uridylate-specific endoribonuclease / 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 / Coronavirus 3Ecto domain profile. / : / 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 (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
Similarity search - Domain/homology
Replicase polyprotein 1ab / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSARS CORONAVIRUS HKU-39849
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsSutton, G. / Fry, E. / Carter, L. / Sainsbury, S. / Walter, T. / Nettleship, J. / Berrow, N. / Owens, R. / Gilbert, R. / Davidson, A. ...Sutton, G. / Fry, E. / Carter, L. / Sainsbury, S. / Walter, T. / Nettleship, J. / Berrow, N. / Owens, R. / Gilbert, R. / Davidson, A. / Siddell, S. / Poon, L.L.M. / Diprose, J. / Alderton, D. / Walsh, M. / Grimes, J.M. / Stuart, D.I.
CitationJournal: Structure / Year: 2004
Title: The Nsp9 Replicase Protein of Sars-Coronavirus, Structure and Functional Insights
Authors: Sutton, G. / Fry, E. / Carter, L. / Sainsbury, S. / Walter, T. / Nettleship, J. / Berrow, N. / Owens, R. / Gilbert, R. / Davidson, A. / Siddell, S. / Poon, L.L.M. / Diprose, J. / Alderton, D. ...Authors: Sutton, G. / Fry, E. / Carter, L. / Sainsbury, S. / Walter, T. / Nettleship, J. / Berrow, N. / Owens, R. / Gilbert, R. / Davidson, A. / Siddell, S. / Poon, L.L.M. / Diprose, J. / Alderton, D. / Walsh, M. / Grimes, J.M. / Stuart, D.I.
History
DepositionJan 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NSP9


Theoretical massNumber of molelcules
Total (without water)16,0001
Polymers16,0001
Non-polymers00
Water0
1
A: NSP9

A: NSP9


Theoretical massNumber of molelcules
Total (without water)32,0002
Polymers32,0002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area2430 Å2
ΔGint-19.2 kcal/mol
Surface area12940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.000, 58.000, 85.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322

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Components

#1: Protein NSP9 / PP1AB / ORF1AB / REPLICASE POLYPROTEIN 1AB


Mass: 16000.195 Da / Num. of mol.: 1 / Fragment: NSP9, RESIDUES 3925-4037
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS CORONAVIRUS HKU-39849 / Cell line: VERO E6 / Plasmid: GATEWAY / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834(DE3) / References: UniProt: P59641, UniProt: P0C6X7*PLUS
Compound detailsFUNCTION: PART OF THE REPLICASE COMPLEX
Sequence detailsTHE 30 N-TERMINAL RESIDUES ARE THE N-TERMINAL TAG. THE FIRST NINE RESIDUES OF THE ENTRY CORRESPOND ...THE 30 N-TERMINAL RESIDUES ARE THE N-TERMINAL TAG. THE FIRST NINE RESIDUES OF THE ENTRY CORRESPOND TO PART OF THE N-TERMINAL TAG ADDED TO FACILITATE PURIFICATION AND ARE NOT PART OF THE NATIVE PROTEIN.

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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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 3.8
Details: 100MM CITRATE/PHOSPHATE PH3.8, 20% PEG 8000, PROTEIN CONCENTRATION 10MG/ML SITTING DROP 100NL + 100NL, pH 3.80
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMTris-HCl1drop
2100 mM1dropNaCl
32 mMdithiothreitol1droppH8.0
410 mg/mlprotein1drop
5100 mMcitrate phosphate1reservoirpH3.8
620 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8856, 0.97829, 0.99988
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2003 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.88561
20.978291
30.999881
ReflectionResolution: 2.8→20 Å / Num. obs: 3908 / % possible obs: 100 % / Redundancy: 24 % / Rmerge(I) obs: 0.19 / Net I/σ(I): 20
Reflection shellResolution: 2.8→2.9 Å / Mean I/σ(I) obs: 2 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.8 Å / % possible obs: 100 % / Redundancy: 24 % / Rmerge(I) obs: 0.19
Reflection shell
*PLUS
Highest resolution: 3.3 Å / Lowest resolution: 3.5 Å / % possible obs: 100 % / Redundancy: 25 % / Rmerge(I) obs: 0.48

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVE/RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Data cutoff high absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.314 -5 %RANDOM
Rwork0.228 ---
obs0.228 3892 99.9 %-
Solvent computationSolvent model: MASK / Bsol: 60 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.7 Å2
Refine analyzeLuzzati d res low obs: 20 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms945 0 0 0 945
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it6.33
X-RAY DIFFRACTIONc_mcangle_it9.33
X-RAY DIFFRACTIONc_scbond_it12.55
X-RAY DIFFRACTIONc_scangle_it15.25
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8 /
RfactorNum. reflection
Rfree0.41 33
Rwork0.39 441
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM
Refinement
*PLUS
Rfactor Rfree: 0.294 / Rfactor Rwork: 0.236
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Lowest resolution: 2.9 Å / Rfactor Rfree: 0.405 / Rfactor Rwork: 0.385

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