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- PDB-3zbd: Structure of TGEV nsp1 -

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Basic information

Entry
Database: PDB / ID: 3zbd
TitleStructure of TGEV nsp1
ComponentsNON-STRUCTURAL PROTEIN 1
KeywordsVIRAL PROTEIN / CORONAVIRUS / ALPHACORONAVIRUS / NSP1
Function / homology
Function and homology information


host cell membrane / viral genome replication / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm ...host cell membrane / viral genome replication / transferase activity / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / symbiont-mediated perturbation of host ubiquitin-like protein modification / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / host cell perinuclear region of cytoplasm / viral protein processing / induction by virus of host autophagy / cysteine-type endopeptidase activity / virus-mediated perturbation of host defense response / proteolysis / RNA binding / zinc ion binding / membrane
Similarity search - Function
Replicase polyprotein 1a / Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / SH3 type barrels. / Papain-like protease, N-terminal domain superfamily, coronavirus / : ...Replicase polyprotein 1a / Alphacoronavirus nsp1 / Replicase polyprotein N-term from Coronavirus nsp1 / Alphacoronavirus nsp1 domain superfamily / Non-structural protein 5, alphacoronavirus / Non-structural protein 6, alphacoronavirus / Nonstructural protein 2, HCoV-229E-like / SH3 type barrels. / 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 / Peptidase C30, domain 3, coronavirus / Non-structural protein 6, coronavirus / Coronavirus replicase NSP3, C-terminal / Non-structural protein NSP4, N-terminal, coronavirus / Coronavirus endopeptidase C30 / Coronavirus papain-like peptidase / Coronavirus replicase NSP8 / Coronavirus RNA synthesis protein NSP10 / Coronavirus replicase NSP4, C-terminal / Coronavirus replicase NSP6 / Coronavirus replicase NSP4, N-terminal / Coronavirus replicase NSP3, C-terminal / Coronavirus main protease (M-pro) domain profile. / Coronavirus replicase NSP9 / Non-structural protein 3, X-domain-like / Macro domain / Appr-1"-p processing enzyme / Macro domain / Macro domain profile. / Macro domain-like / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Mainly Beta
Similarity search - Domain/homology
Replicase polyprotein 1a
Similarity search - Component
Biological speciesPORCINE TRANSMISSIBLE GASTROENTERITIS CORONAVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.49 Å
AuthorsJansson, A.M.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of Alphacoronavirus Tgev Nsp1 Has Implications for Coronavirus Nsp1 Function and Evolution.
Authors: Jansson, A.M.
History
DepositionNov 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NON-STRUCTURAL PROTEIN 1
B: NON-STRUCTURAL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)26,0422
Polymers26,0422
Non-polymers00
Water3,729207
1
A: NON-STRUCTURAL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)13,0211
Polymers13,0211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NON-STRUCTURAL PROTEIN 1


Theoretical massNumber of molelcules
Total (without water)13,0211
Polymers13,0211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.640, 36.090, 42.270
Angle α, β, γ (deg.)91.49, 108.85, 94.20
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NON-STRUCTURAL PROTEIN 1 / NSP1 / P9


Mass: 13020.944 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PORCINE TRANSMISSIBLE GASTROENTERITIS CORONAVIRUS
Strain: PURDUE / Plasmid: PEXP5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21-AI / References: UniProt: P0C6V2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAIN 1 (1-110) FEATURE IDENTIFIER PRO_0000338303

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growDetails: 5%(V/VOL) PEG 4000, 200MM AMMONIUM CHLORIDE, 30MM HEPES, 30MM MES, PH 6.2

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF ID23-210.873
SYNCHROTRONESRF ID14-421.072
Detector
TypeIDDetector
MARRESEARCH1CCD
MARRESEARCH2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.8731
21.0721
ReflectionResolution: 1.5→27.4 Å / Num. obs: 30811 / % possible obs: 96.6 % / Observed criterion σ(I): 1.5 / Redundancy: 4 % / Biso Wilson estimate: 17.72 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.3
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 95.4

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 1.49→26.05 Å / Cor.coef. Fo:Fc: 0.9592 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.077 / SU Rfree Blow DPI: 0.079 / SU Rfree Cruickshank DPI: 0.078
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 1535 4.91 %RANDOM
Rwork0.1747 ---
obs0.1763 31262 96.38 %-
Displacement parametersBiso mean: 23.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.7484 Å20.2673 Å21.786 Å2
2--1.4061 Å2-1.9738 Å2
3----2.1545 Å2
Refine analyzeLuzzati coordinate error obs: 0.181 Å
Refinement stepCycle: LAST / Resolution: 1.49→26.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 0 207 1925
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011755HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.062379HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d611SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes52HARMONIC2
X-RAY DIFFRACTIONt_gen_planes250HARMONIC5
X-RAY DIFFRACTIONt_it1755HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.68
X-RAY DIFFRACTIONt_other_torsion15.16
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion213SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2019SEMIHARMONIC4
LS refinement shellResolution: 1.49→1.54 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2471 132 4.9 %
Rwork0.2056 2562 -
all0.2076 2694 -
obs--96.38 %
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)
10.7724-0.2262-0.02492.3685-0.12320.6886-0.0092-0.02050.08970.1839-0.013-0.32660.04370.04680.0222-0.0655-0.0055-0.0334-0.0460.0162-0.0008-22.1337-4.596527.4639
21.5025-0.15920.20372.9809-0.87951.16360.00960.1195-0.0023-0.3587-0.005-0.04630.08980.0585-0.0045-0.00980.01610.0165-0.0373-0.0033-0.0877-14.536713.509549.6154
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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