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- PDB-1q31: Crystal Structure of the Tobacco Etch Virus Protease C151A mutant -

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Basic information

Entry
Database: PDB / ID: 1q31
TitleCrystal Structure of the Tobacco Etch Virus Protease C151A mutant
ComponentsNuclear inclusion protein A
KeywordsViral protein / hydrolase / 3C-type protease / TEV / two-domain / antiparallel / beta-barrel / trypsin-like / C151A
Function / homology
Function and homology information


nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated suppression of host innate immune response ...nuclear-inclusion-a endopeptidase / helper-component proteinase / hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / host cell cytoplasmic vesicle / helical viral capsid / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / symbiont-mediated suppression of host innate immune response / RNA-directed RNA polymerase / viral translational frameshifting / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / structural molecule activity / proteolysis / RNA binding / ATP binding
Similarity search - Function
Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein ...Helper component proteinase / Peptidase S30, polyprotein P1, potyvirus / Polyprotein, Potyviridae / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain / Potyviral polyprotein protein 3 / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily / Helper component proteinase / Peptidase family C4 / Potyvirus P1 protease / Potyviridae polyprotein / Protein P3 of Potyviral polyprotein / Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain profile. / Potyviridae P1 protease domain profile. / Potyvirus NIa protease (NIa-pro) domain / Potyvirus NIa protease (NIa-pro) domain profile. / Potyvirus coat protein / Potyvirus coat protein / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Trypsin-like serine proteases / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Thrombin, subunit H / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Genome polyprotein
Similarity search - Component
Biological speciesTobacco etch virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNunn, C.M. / Djordjevic, S. / George, R.R. / Urquhart, G.T. / Chao, L.H. / Tsuchiya, Y.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of tobacco etch virus protease shows the protein C terminus bound within the active site.
Authors: Nunn, C.M. / Jeeves, M. / Cliff, M.J. / Urquhart, G.T. / George, R.R. / Chao, L.H. / Tscuchia, Y. / Djordjevic, S.
History
DepositionJul 28, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear inclusion protein A
B: Nuclear inclusion protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2114
Polymers55,0542
Non-polymers1562
Water66737
1
A: Nuclear inclusion protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6052
Polymers27,5271
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Nuclear inclusion protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6052
Polymers27,5271
Non-polymers781
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Nuclear inclusion protein A
hetero molecules

B: Nuclear inclusion protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2114
Polymers55,0542
Non-polymers1562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area3180 Å2
ΔGint-24 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.587, 41.544, 96.063
Angle α, β, γ (deg.)90.00, 108.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-911-

HOH

DetailsThe biological assemply comprises 2 protomers of TEV protease which are similar in conformation and related by non-crystallographic symmetry.

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Components

#1: Protein Nuclear inclusion protein A / Tobacco Etch Virus Protease


Mass: 27527.168 Da / Num. of mol.: 2 / Mutation: C151A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco etch virus / Genus: Potyvirus / Plasmid: PRET3ATEV / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3)
References: UniProt: P04517, nuclear-inclusion-a endopeptidase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.68 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: lithium sulphate monohydrate, Tris HCL, PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2002
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→91 Å / Num. all: 15262 / Num. obs: 13436 / % possible obs: 88 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.7→2.8 Å / % possible all: 93.5

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1LVB

1lvb


Resolution: 2.7→36.58 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.302 1364 RANDOM
Rwork0.24 --
obs0.24 13436 -
all-15447 -
Displacement parametersBiso mean: 74.55 Å2
Baniso -1Baniso -2Baniso -3
1--39.08 Å20 Å27.92 Å2
2--33.83 Å20 Å2
3---5.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.73 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.7→36.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3635 0 8 37 3680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.72
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.7-2.820.441360.390.038115459.8
2.82-2.970.4851430.3930.041132370.3
2.97-3.160.3881610.3190.031155881.5
3.16-3.40.341700.2850.026172990.5
3.4-3.740.3411770.2510.026186696.3
3.74-4.290.2681790.2050.02186697.7

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