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- PDB-3ub0: Crystal structure of the nonstructural protein 7 and 8 complex of... -

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Basic information

Entry
Database: PDB / ID: 3ub0
TitleCrystal structure of the nonstructural protein 7 and 8 complex of Feline Coronavirus
Components
  • Non-structural protein 6, nsp6,
  • Non-structural protein 7, nsp7
KeywordsREPLICATION / Feline Coronavirus / nonstructural protein / primer-independent RNA polymerase
Function / homology
Function and homology information


host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity ...host cell membrane / viral genome replication / Lyases; Phosphorus-oxygen lyases / Hydrolases; Acting on ester bonds; Exoribonucleases producing 5'-phosphomonoesters / 5'-3' DNA helicase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / 3'-5'-RNA exonuclease activity / mRNA guanylyltransferase / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / endonuclease activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / DNA helicase / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / lyase activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane
Similarity search - Function
Helix Hairpins - #2090 / Nsp8 replicase, head domain / Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / : / Nonstructural protein 14, alphacoronavirus / RNA-dependent RNA polymerase, alphacoronavirus / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus ...Helix Hairpins - #2090 / Nsp8 replicase, head domain / Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / 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 / Helix Hairpins / Helix non-globular / Special / 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. / Papain-like protease, N-terminal domain superfamily, coronavirus / : / Coronavirus 3Ecto domain profile. / : / 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 / NSP3, second ubiquitin-like (Ubl) domain, coronavirus / Coronavirus Nsp4 C-terminal (Nsp4C) domain profile. / Papain-like protease, thumb domain superfamily, coronavirus / Coronavirus replicase NSP7 / Peptidase family C16 domain profile. / Non-structural protein NSP7, coronavirus / Peptidase C30, coronavirus / Peptidase C16, coronavirus / Non-structural protein NSP9, 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
Similarity search - Domain/homology
Replicase polyprotein 1ab
Similarity search - Component
Biological speciesFeline infectious peritonitis virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsXiao, Y. / Hilgenfeld, R. / Ma, Q.
CitationJournal: J.Virol. / Year: 2012
Title: Nonstructural proteins 7 and 8 of feline coronavirus form a 2:1 heterotrimer that exhibits primer-independent RNA polymerase activity.
Authors: Xiao, Y. / Ma, Q. / Restle, T. / Shang, W. / Svergun, D.I. / Ponnusamy, R. / Sczakiel, G. / Hilgenfeld, R.
History
DepositionOct 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-structural protein 6, nsp6,
B: Non-structural protein 7, nsp7
C: Non-structural protein 7, nsp7
D: Non-structural protein 6, nsp6,
E: Non-structural protein 7, nsp7
F: Non-structural protein 7, nsp7


Theoretical massNumber of molelcules
Total (without water)83,0506
Polymers83,0506
Non-polymers00
Water1,38777
1
A: Non-structural protein 6, nsp6,
B: Non-structural protein 7, nsp7
C: Non-structural protein 7, nsp7


Theoretical massNumber of molelcules
Total (without water)41,5253
Polymers41,5253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-61 kcal/mol
Surface area18940 Å2
MethodPISA
2
D: Non-structural protein 6, nsp6,
E: Non-structural protein 7, nsp7
F: Non-structural protein 7, nsp7


Theoretical massNumber of molelcules
Total (without water)41,5253
Polymers41,5253
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-59 kcal/mol
Surface area19220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.454, 160.301, 102.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Non-structural protein 6, nsp6, / Replicase polyprotein 1ab


Mass: 22020.658 Da / Num. of mol.: 2 / Fragment: unp residues 3583-3777
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline infectious peritonitis virus / Strain: FIPV WSU-79/1146 / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) / References: UniProt: Q98VG9
#2: Protein
Non-structural protein 7, nsp7 / Replicase polyprotein 1ab


Mass: 9752.201 Da / Num. of mol.: 4 / Fragment: unp residues 3500-3582
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline infectious peritonitis virus / Strain: FIPV WSU-79/1146 / Gene: rep, 1a-1b / Production host: Escherichia coli (E. coli) / References: UniProt: Q98VG9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.01 Å3/Da / Density % sol: 59.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.7
Details: 2.24M (NH4)2HPO4, 2mM TCEP, 0.1M Tris-HCl, pH 8.7, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9809
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Mar 8, 2011
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 2.6→33.45 Å / Num. all: 31155 / Num. obs: 31155 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.23 % / Biso Wilson estimate: 73.59 Å2 / Rmerge(I) obs: 0.0577 / Rsym value: 0.0577 / Net I/σ(I): 20.38
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 7.41 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.33 / Rsym value: 0.62 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
SHELXDphasing
SHELXEmodel building
BUSTER2.11.1refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.6→33.45 Å / Cor.coef. Fo:Fc: 0.9403 / Cor.coef. Fo:Fc free: 0.9417 / SU R Cruickshank DPI: 0.422 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: auto-BUSTER
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1471 4.72 %thin shells
Rwork0.2051 ---
all0.2062 31155 --
obs0.2062 31155 99.97 %-
Displacement parametersBiso mean: 86.3 Å2
Baniso -1Baniso -2Baniso -3
1-9.067 Å20 Å20 Å2
2--0.2469 Å20 Å2
3----9.3139 Å2
Refine analyzeLuzzati coordinate error obs: 0.454 Å
Refinement stepCycle: LAST / Resolution: 2.6→33.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5498 0 0 77 5575
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015579HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.297546HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1992SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes151HARMONIC2
X-RAY DIFFRACTIONt_gen_planes775HARMONIC5
X-RAY DIFFRACTIONt_it5579HARMONIC20
X-RAY DIFFRACTIONt_omega_torsion2.67
X-RAY DIFFRACTIONt_other_torsion21.82
X-RAY DIFFRACTIONt_chiral_improper_torsion761SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact6220SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.69 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0 0 0 %
Rwork0.2478 2831 -
all0.2478 2831 -
obs--99.97 %
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)
15.3064.848-2.13346.2967-2.58681.5270.3603-0.3199-0.2810.6981-0.32680.1458-0.1352-0.2017-0.03350.2306-0.11390.00670.3746-0.00560.259278.743950.933349.9213
21.53760.1430.35914.64291.54691.818-0.04630.38950.0694-0.39590.0815-0.1316-0.10610.1028-0.03530.189-0.07020.07420.45450.09780.170940.98952.592234.8954
35.46952.9297-0.86854.1886-0.16621.41090.07550.16930.3935-0.09390.0363-0.2223-0.342-0.0109-0.11180.1903-0.09660.01230.23050.14710.419953.445133.946946.895
44.07612.0840.14934.50771.37864.67670.01250.1221-0.0848-0.17340.1159-0.4346-0.13880.0536-0.12840.0376-0.03950.03060.13620.07040.085145.276615.859239.9273
52.64911.5221-0.72851.8286-0.78161.7732-0.17710.374-0.9136-0.20980.0587-0.44650.2841-0.3590.11840.18990.00110.04180.4288-0.0720.397177.706541.415938.1459
62.1994-1.6395-0.25498.29284.06323.5768-0.45431.08630.958-1.09650.92310.5242-2.2596-1.8311-0.46880.33580.4563-0.23350.97810.598-0.283873.286179.404111.4992
73.21332.4062-1.60335.4844-2.68744.7967-0.57330.8579-1.3035-0.79440.0304-0.67080.86730.02860.5430.3492-0.15010.25620.523-0.37680.616983.663639.37731.6312
88.27111.3334-1.15333.096-0.29963.6952-0.28191.7383-0.1296-0.49520.2625-0.0105-0.0923-0.79190.01940.1404-0.1019-0.02930.9241-0.0779-0.008181.114657.81321.3022
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|-2 - A|72 }A-2 - 72
2X-RAY DIFFRACTION2{ A|73 - A|192 }A73 - 192
3X-RAY DIFFRACTION3{ B|2 - B|83 }B2 - 83
4X-RAY DIFFRACTION4{ C|1 - C|81 }C1 - 81
5X-RAY DIFFRACTION5{ D|-2 - D|138 }D-2 - 138
6X-RAY DIFFRACTION6{ D|139 - D|191 }D139 - 191
7X-RAY DIFFRACTION7{ E|2 - E|82 }E2 - 82
8X-RAY DIFFRACTION8{ F|1 - F|77 }F1 - 77

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