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- PDB-2h85: Crystal Structure of Nsp 15 from SARS -

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Entry
Database: PDB / ID: 2h85
TitleCrystal Structure of Nsp 15 from SARS
ComponentsPutative orf1ab polyprotein
KeywordsVIRAL PROTEIN / endoribonuclease / SARS / RNA / nsp
Function / homology
Function and homology information


cysteine-type deubiquitinase activity => GO:0004843 / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / exonuclease activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity ...cysteine-type deubiquitinase activity => GO:0004843 / Assembly of the SARS-CoV-1 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / Transcription of SARS-CoV-1 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / Replication of the SARS-CoV-1 genome / K48-linked deubiquitinase activity / exonuclease activity / host cell endoplasmic reticulum / K63-linked deubiquitinase activity / SARS-CoV-1 modulates host translation machinery / viral transcription / host cell membrane / endoplasmic reticulum-Golgi intermediate compartment / DNA helicase activity / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / SARS-CoV-1 activates/modulates innate immune responses / 5'-3' RNA helicase activity / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / : / methylation / double membrane vesicle viral factory outer membrane / SARS coronavirus main proteinase / host cell endosome / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase 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 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / single-stranded RNA binding / membrane => GO:0016020 / host cell perinuclear region of cytoplasm / 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
Nsp15 N-terminal domain-like / nsp15 middle domain / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / Double Stranded RNA Binding Domain / RNA-dependent RNA polymerase, SARS-CoV-like / Nonstructural protein 14, betacoronavirus / NSP15, NendoU domain, coronavirus / : / : ...Nsp15 N-terminal domain-like / nsp15 middle domain / Non-structural protein 3, SUD-N macrodomain, SARS-CoV / Viral (Superfamily 1) RNA helicase / Double Stranded RNA Binding Domain / 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.
Similarity search - Domain/homology
Replicase polyprotein 1ab / 2'-O-methyltransferase
Similarity search - Component
Biological speciesSARS coronavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsRicagno, S. / Egloff, M.P. / Ulferts, R. / Coutard, B. / Nurizzo, D. / Campanacci, V. / Cambillau, C. / Ziebuhr, J. / Canard, B.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: Crystal structure and mechanistic determinants of SARS coronavirus nonstructural protein 15 define an endoribonuclease family.
Authors: Ricagno, S. / Egloff, M.P. / Ulferts, R. / Coutard, B. / Nurizzo, D. / Campanacci, V. / Cambillau, C. / Ziebuhr, J. / Canard, B.
History
DepositionJun 6, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative orf1ab polyprotein


Theoretical massNumber of molelcules
Total (without water)38,5711
Polymers38,5711
Non-polymers00
Water1,58588
1
A: Putative orf1ab polyprotein
x 6


Theoretical massNumber of molelcules
Total (without water)231,4256
Polymers231,4256
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation14_666-y+5/4,-x+5/4,-z+5/41
crystal symmetry operation19_666-x+5/4,-z+5/4,-y+5/41
crystal symmetry operation24_666-z+5/4,-y+5/4,-x+5/41
Buried area18010 Å2
ΔGint-105 kcal/mol
Surface area84530 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)166.584, 166.584, 166.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein Putative orf1ab polyprotein


Mass: 38570.828 Da / Num. of mol.: 1 / Mutation: V291G, D300G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SARS coronavirus / Genus: Coronavirus / Strain: Frankfurt-1 / Gene: Nsp15 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q6VA80, UniProt: P0C6X7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 4.99 Å3/Da / Density % sol: 75.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 5-20% PEG 10000, 0.2M imidazole malate pH 9.0-10.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97938 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 3, 2005
RadiationMonochromator: Silicon (1 1 1) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.6→52 Å / Num. all: 24505 / Num. obs: 24505 / % possible obs: 98.9 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.169 / Net I/σ(I): 11.8
Reflection shellResolution: 2.6→2.667 Å / Redundancy: 12 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
MOSFLMdata reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→52.7 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.679 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.261 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24008 1266 5.1 %RANDOM
Rwork0.20758 ---
obs0.2092 23625 100 %-
all-24505 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.339 Å2
Refinement stepCycle: LAST / Resolution: 2.6→52.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2714 0 0 88 2802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222769
X-RAY DIFFRACTIONr_bond_other_d0.0010.022503
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9573753
X-RAY DIFFRACTIONr_angle_other_deg0.77235851
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.37225.285123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.39215483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.562159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2429
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023072
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02534
X-RAY DIFFRACTIONr_nbd_refined0.1940.2550
X-RAY DIFFRACTIONr_nbd_other0.1820.22552
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21388
X-RAY DIFFRACTIONr_nbtor_other0.090.21637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1140.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1840.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2290.29
X-RAY DIFFRACTIONr_mcbond_it0.7121.52197
X-RAY DIFFRACTIONr_mcbond_other0.0821.5708
X-RAY DIFFRACTIONr_mcangle_it0.82622798
X-RAY DIFFRACTIONr_scbond_it1.3331212
X-RAY DIFFRACTIONr_scangle_it2.0664.5955
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 88 -
Rwork0.281 1699 -
obs--100 %

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