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- PDB-2j98: Human coronavirus 229E non structural protein 9 cys69ala mutant (Nsp9) -

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Basic information

Entry
Database: PDB / ID: 2j98
TitleHuman coronavirus 229E non structural protein 9 cys69ala mutant (Nsp9)
Components(REPLICASE POLYPROTEIN 1AB) x 2
KeywordsRNA BINDING PROTEIN / SSB / HCOV / MEMBRANE / HELICASE / SARS COV / VIRAL REPLICASE / RNA REPLICATION / ATP-BINDING / NUCLEOTIDE-BINDING / RIBOSOMAL FRAMESHIFT / RNA-BINDING PROTEIN
Function / homology
Function and homology information


host cell membrane / viral genome replication / transferase activity / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / endonuclease activity / mRNA guanylyltransferase ...host cell membrane / viral genome replication / transferase activity / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / host cell endoplasmic reticulum-Golgi intermediate compartment / 5'-3' DNA helicase activity / 3'-5'-RNA exonuclease activity / endonuclease activity / mRNA guanylyltransferase / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / omega peptidase activity / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / methyltransferase cap1 activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / regulation of autophagy / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / 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 / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Replicase NSP9 / Alphacoronavirus nsp1 domain superfamily / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor ...Replicase NSP9 / Alphacoronavirus nsp1 domain superfamily / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / : / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / AAA domain / Pectin lyase fold/virulence factor / P-type ATPase, transmembrane domain superfamily / 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. / 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. / 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. / Coronavirus (CoV) Nsp3 Y domain profile. / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Coronavirus main protease (M-pro) domain profile. / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, coronavirus / Non-structural protein NSP7, coronavirus / Non-structural protein NSP8, coronavirus / RNA synthesis protein NSP10, coronavirus / Non-structural protein NSP4, C-terminal, coronavirus / RNA synthesis protein NSP10 superfamily, coronavirus / Non-structural protein NSP9 superfamily, coronavirus / Non-structural protein NSP7 superfamily, coronavirus / Non-structural protein NSP8 superfamily, coronavirus / Non-structural protein NSP4, C-terminal superfamily, coronavirus / Papain-like protease, thumb domain superfamily, coronavirus / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Replicase polyprotein 1a / Replicase polyprotein 1ab
Similarity search - Component
Biological speciesHUMAN CORONAVIRUS 229E
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPonnusamy, R. / Mesters, J.R. / Moll, R. / Hilgenfeld, R.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Variable Oligomerization Modes in Coronavirus Non-Structural Protein 9.
Authors: Ponnusamy, R. / Moll, R. / Weimar, T. / Mesters, J.R. / Hilgenfeld, R.
History
DepositionNov 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_residues / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REPLICASE POLYPROTEIN 1AB
B: REPLICASE POLYPROTEIN 1AB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2103
Polymers24,0562
Non-polymers1541
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10.9 kcal/mol
Surface area12890 Å2
MethodPQS
Unit cell
Length a, b, c (Å)26.396, 61.377, 107.309
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9975, -0.0703, -0.000359), (-0.06991, -0.9914, -0.1102), (0.007392, 0.11, -0.9939)
Vector: 0.8273, 53.99, 265.3)

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Components

#1: Protein REPLICASE POLYPROTEIN 1AB / PP1AB / ORF1AB POLYPROTEIN / NON STRUCTURAL PROTEIN 9 MUTANT


Mass: 12028.768 Da / Num. of mol.: 1 / Fragment: RESIDUES 3825-3933 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN CORONAVIRUS 229E / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C6U2, UniProt: P0C6X1*PLUS
#2: Protein REPLICASE POLYPROTEIN 1AB / PP1AB / ORF1AB POLYPROTEIN / NON STRUCTURAL PROTEIN 9 MUTANT


Mass: 12026.752 Da / Num. of mol.: 1 / Fragment: RESIDUES 3825-3933 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN CORONAVIRUS 229E / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0C6U2, UniProt: P0C6X1*PLUS
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 3893 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 3893 TO ALA

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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: 1.85 Å3/Da / Density % sol: 33.08 % / Description: NONE
Crystal growpH: 4.5 / Details: 0.1M NA ACETATE PH 4.6 30% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8075
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 18, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8075 Å / Relative weight: 1
ReflectionResolution: 1.74→30 Å / Num. obs: 17889 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.9
Reflection shellResolution: 1.74→1.8 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.07 / % possible all: 44.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKLSUITEdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QZ8

1qz8


Resolution: 1.8→53.68 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.371 / SU ML: 0.113 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 1,2 AND 107,108 FROM CHAIN A, RESIDUES 1-4 FROM CHAIN B ARE DISORDERED.CHAIN A RESIDUES 55REMARK OCCUPANCIES SET TO ZERO. VIZIER. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.RESIDUES 1,2 AND 107,108 FROM CHAIN A, RESIDUES 1-4 FROM CHAIN B ARE DISORDERED.CHAIN A RESIDUES 55REMARK OCCUPANCIES SET TO ZERO. VIZIER.VIRAL ENZYMES INVOLVED IN REPLICATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1125 6.7 %RANDOM
Rwork0.214 ---
obs0.218 15696 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.52 Å20 Å2
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→53.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 8 74 1687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221619
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.982184
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9585202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39723.49263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04415276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.52159
X-RAY DIFFRACTIONr_chiral_restr0.1210.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021205
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.2707
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21095
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.282
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.247
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3820.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.071.51028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73521614
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9213681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1534.5570
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 83 -
Rwork0.246 1136 -
obs--99.51 %
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)
14.1849-0.3797-0.02522.75280.14961.1411-0.0208-0.1631-0.19280.25070.02030.0170.14850.03530.0005-0.06480.0033-0.0188-0.07640.0118-0.07295.348618.4814147.0995
23.05740.0108-0.56442.5515-0.4271.40180.0326-0.02730.0621-0.1991-0.03780.0661-0.1426-0.0340.0052-0.05940.01-0.0251-0.076-0.0406-0.07756.322722.5195120.6709
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 108
2X-RAY DIFFRACTION2B6 - 106

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