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- PDB-1qz8: Crystal structure of SARS coronavirus NSP9 -

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Basic information

Entry
Database: PDB / ID: 1qz8
TitleCrystal structure of SARS coronavirus NSP9
Componentspolyprotein 1ab
KeywordsUNKNOWN FUNCTION / SARS / replication / NSP9 / coronavirus
Function / homology
Function and homology information


viral RNA-directed RNA polymerase complex / viral replication complex formation and maintenance / exoribonuclease complex / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation ...viral RNA-directed RNA polymerase complex / viral replication complex formation and maintenance / exoribonuclease complex / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / : / cytoplasmic viral factory / positive regulation of ubiquitin-specific protease activity / symbiont-mediated suppression of host translation / : / : / endopeptidase complex / endoribonuclease complex / mRNA capping enzyme complex / positive stranded viral RNA replication / positive regulation of RNA biosynthetic process / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / protein K48-linked deubiquitination / Translation of Replicase and Assembly of the Replication Transcription Complex / K48-linked deubiquitinase activity / Replication of the SARS-CoV-1 genome / protein K63-linked deubiquitination / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / RNA-templated transcription / viral transcription / SARS-CoV-1 modulates host translation machinery / protein autoprocessing / 7-methylguanosine mRNA capping / membrane => GO:0016020 / 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 / 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 / endonuclease 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 / 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 / host cell cytoplasm / 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 / protein dimerization activity / regulation of autophagy / viral protein processing / host cell perinuclear region of cytoplasm / lyase activity / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated suppression of host gene expression / 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 / ATP hydrolysis activity / proteolysis / zinc ion binding / ATP binding / identical protein binding / membrane
Similarity search - Function
Replicase NSP9 / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral superfamily 1 RNA helicase core domain / 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. ...Replicase NSP9 / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral superfamily 1 RNA helicase core domain / 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 / : / 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 / 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. / : / : / Coronavirus replicase NSP7 / Coronavirus 3Ecto domain profile.
Similarity search - Domain/homology
Replicase polyprotein 1ab / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsEgloff, M.P. / Ferron, F. / Campanacci, V. / Longhi, S. / Rancurel, C. / Dutartre, H. / Snijder, E.J. / Gorbalenya, A.E. / Cambillau, C. / Canard, B.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: The severe acute respiratory syndrome-coronavirus replicative protein nsp9 is a single-stranded RNA-binding subunit unique in the RNA virus world.
Authors: Egloff, M.P. / Ferron, F. / Campanacci, V. / Longhi, S. / Rancurel, C. / Dutartre, H. / Snijder, E.J. / Gorbalenya, A.E. / Cambillau, C. / Canard, B.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structural genomics of the SARS coronavirus: cloning, expression, crystallization and preliminary crystallographic study of the NSP9 protein
Authors: CAMPANACCI, V. / EGLOFF, M.P. / LONGHI, S. / FERRON, F. / RANCUREL, C. / SALOMONI, A. / DUROUSSEAU, C. / TOCQUE, F. / BREMOND, N. / DOBBE, J.C. / SNIJDER, E.J. / CANARD, B. / CAMBILLAU, C.
History
DepositionSep 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: polyprotein 1ab
B: polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2156
Polymers24,8302
Non-polymers3844
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-73 kcal/mol
Surface area12170 Å2
MethodPISA
2
A: polyprotein 1ab
B: polyprotein 1ab
hetero molecules

A: polyprotein 1ab
B: polyprotein 1ab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,42912
Polymers49,6614
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_556-x+y,y,-z+3/21
Buried area5900 Å2
ΔGint-167 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.115, 89.115, 136.675
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNASNASN4AA11 - 3311 - 33
21GLNGLNASNASN4BB11 - 3311 - 33
32ASNASNVALVAL6AA34 - 4134 - 41
42ASNASNVALVAL6BB34 - 4134 - 41
53LEULEUALAALA3AA42 - 5442 - 54
63LEULEUALAALA3BB42 - 5442 - 54
74ARGARGTHRTHR4AA55 - 6455 - 64
84ARGARGTHRTHR4BB55 - 6455 - 64
95ILEILEPHEPHE3AA65 - 7565 - 75
105ILEILEPHEPHE3BB65 - 7565 - 75
116PHEPHELYSLYS6AA75 - 8675 - 86
126PHEPHELYSLYS6BB75 - 8675 - 86
137TYRTYRASNASN3AA87 - 9587 - 95
147TYRTYRASNASN3BB87 - 9587 - 95
158ASNASNGLNGLN4AA96 - 11396 - 113
168ASNASNGLNGLN4BB96 - 11396 - 113

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Components

#1: Protein polyprotein 1ab / NSP9


Mass: 12415.133 Da / Num. of mol.: 2 / Fragment: SARS coronavirus NSP9, residues 4118-4230
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Strain: Frankfurt 1 / Gene: NSP9 / Plasmid details: Gateway system / Plasmid: PDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)PLysS / References: UniProt: P59641, UniProt: P0C6X7*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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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: 3.1 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: Ammonium Sulphate, Na Citrate, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Details: Campanacci, V., (2003) Acta Crystallogr.,Sect.D, 59, 1628.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12.0 Mammonium sulfate1drop
20.1 Mphosphate-citrate1droppH4.2
35.8 mg/mlprotein1drop
41.8-2.2 Mammonium sulfate1reservoirpH4.0-4.5
50.1 Mphosphate-citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 18, 2003
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→14.9 Å / Num. all: 9345 / Num. obs: 9345 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Rsym value: 0.056 / Net I/σ(I): 9.4
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 1.6 / % possible all: 99.1
Reflection
*PLUS
Lowest resolution: 3 Å / Num. measured all: 100668 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→15 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.892 / SU B: 12.262 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.688 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28035 443 4.8 %RANDOM
Rwork0.24792 ---
all0.24955 9345 --
obs0.24951 8724 98.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.181 Å2
Baniso -1Baniso -2Baniso -3
1--2.23 Å2-1.11 Å20 Å2
2---2.23 Å20 Å2
3---3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1699 0 20 31 1750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211749
X-RAY DIFFRACTIONr_bond_other_d0.0020.021578
X-RAY DIFFRACTIONr_angle_refined_deg1.881.9832374
X-RAY DIFFRACTIONr_angle_other_deg1.0133675
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.195219
X-RAY DIFFRACTIONr_chiral_restr0.1120.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021921
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02349
X-RAY DIFFRACTIONr_nbd_refined0.2020.2329
X-RAY DIFFRACTIONr_nbd_other0.2430.21878
X-RAY DIFFRACTIONr_nbtor_other0.0990.21207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.236
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3660.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.23
X-RAY DIFFRACTIONr_mcbond_it0.8681.51097
X-RAY DIFFRACTIONr_mcangle_it1.66321760
X-RAY DIFFRACTIONr_scbond_it2.1433652
X-RAY DIFFRACTIONr_scangle_it3.4514.5614
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
195tight positional0.070.05
671medium positional0.870.5
644loose positional0.935
195tight thermal0.120.5
671medium thermal0.52
644loose thermal3.2510
LS refinement shellResolution: 2.7→2.768 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 25
Rwork0.297 623
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)
12.02511.27771.62834.4252.38023.311-0.07380.01150.11750.10550.135-0.1861-0.08950.1656-0.06120.2243-0.0022-0.03810.1027-0.05040.09078.721567.378791.9774
25.37770.65180.07593.73670.11531.59920.03040.03060.2612-0.2097-0.01640.00020.2424-0.2612-0.0140.1530.01010.03020.08520.08060.0792-13.943262.106377.87
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1133 - 113
2X-RAY DIFFRACTION2BB4 - 1134 - 113
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 15 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.271 / Rfactor Rwork: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.88

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