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- PDB-1lvb: CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH... -

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Basic information

Entry
Database: PDB / ID: 1lvb
TitleCATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH SUBSTRATE
Components
  • CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
  • OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
KeywordsVIRAL PROTEIN / Beta Barrel / Protein-Peptide Complex / Chymotrypsin-like Cystein Protease
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 / Thrombin, subunit H / Helicase superfamily 1/2, ATP-binding domain / 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
Biological speciesTobacco etch virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsPhan, J. / Zdanov, A. / Evdokimov, A.G. / Tropea, J.E. / Peters III, H.K. / Kapust, R.B. / Li, M. / Wlodawer, A. / Waugh, D.S.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural basis for the substrate specificity of tobacco etch virus protease.
Authors: Phan, J. / Zdanov, A. / Evdokimov, A.G. / Tropea, J.E. / Peters III, H.K. / Kapust, R.B. / Li, M. / Wlodawer, A. / Waugh, D.S.
History
DepositionMay 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 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 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5126
Polymers58,3284
Non-polymers1842
Water3,261181
1
A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2563
Polymers29,1642
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-8 kcal/mol
Surface area10570 Å2
MethodPISA
2
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2563
Polymers29,1642
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-9 kcal/mol
Surface area10550 Å2
MethodPISA
3
A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules

A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules

A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules

A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)234,04824
Polymers233,31116
Non-polymers7378
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area26620 Å2
ΔGint-135 kcal/mol
Surface area73700 Å2
MethodPISA
4
A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules

A: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
C: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
B: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)
D: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,02412
Polymers116,6568
Non-polymers3684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area12790 Å2
ΔGint-60 kcal/mol
Surface area37370 Å2
MethodPISA
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-28 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.317, 125.317, 127.933
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)


Mass: 28004.715 Da / Num. of mol.: 2 / Mutation: C151A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tobacco etch virus / Genus: Potyvirus / Plasmid: pRK529 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P04517
#2: Protein/peptide OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE


Mass: 1159.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
References: UniProt: P04517
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.3 Å3/Da / Density % sol: 71.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 6000, Tris, pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113.5 mg/mlprotein1drop
28 %(w/v)PEG60001reservoir
3100 mMTris-HCl1reservoirpH8.0

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Data collection

DiffractionMean temperature: 112 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9755,0.9794,0.9796
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 19, 2001 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97551
20.97941
30.97961
ReflectionResolution: 2.2→50 Å / Num. all: 51139 / Num. obs: 38759 / % possible obs: 93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.2→2.28 Å / % possible all: 90.3
Reflection
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. obs: 51139 / % possible obs: 97.8 % / Rmerge(I) obs: 0.08

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 2.2→33.69 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 272840.06 / Data cutoff high rms absF: 272840.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 2411 5 %RANDOM
Rwork0.236 ---
all-38759 --
obs-38759 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.6121 Å2 / ksol: 0.360486 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1--7.47 Å20 Å20 Å2
2---7.47 Å20 Å2
3---14.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.2→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3590 0 12 181 3783
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it2.051.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it2.182
X-RAY DIFFRACTIONc_scangle_it3.152.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.435 400 5.6 %
Rwork0.394 6703 -
obs--83 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3TOPP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 50 Å / Num. reflection obs: 45949
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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