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- PDB-2jqf: Full Length Leader Protease of Foot and Mouth Disease Virus C51A ... -

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Basic information

Entry
Database: PDB / ID: 2jqf
TitleFull Length Leader Protease of Foot and Mouth Disease Virus C51A Mutant
ComponentsGenome polyprotein
KeywordsVIRAL PROTEIN / Cysteine / Protease / Leader / Foot and Mouth Disease Virus / Oligimerisation
Function / homology
Function and homology information


L-peptidase / suppression by virus of host type I interferon production / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation ...L-peptidase / suppression by virus of host type I interferon production / modulation by virus of host chromatin organization / ribonucleoside triphosphate phosphatase activity / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / : / nucleoside-triphosphate phosphatase / regulation of translation / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell endoplasmic reticulum membrane / molecular adaptor activity / viral protein processing / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Cysteine proteinases / Cathepsin B; Chain A ...Aphthovirus leader protease (L(pro)) domain profile. / Peptidase C28, foot-and-mouth virus L-proteinase / Foot-and-mouth virus L-proteinase / Foot-and-mouth disease virus VP1 coat / Capsid protein VP4, Picornavirus / Viral protein VP4 subunit / Capsid protein VP4 superfamily, Picornavirus / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Cysteine proteinases / Cathepsin B; Chain A / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Papain-like cysteine peptidase superfamily / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Alpha Beta
Similarity search - Domain/homology
Biological speciesFoot-and-mouth disease virus
MethodSOLUTION NMR / torsion angle dynamics
AuthorsCencic, R. / Mayer, C. / Juliano, M.A. / Juliano, L. / Konrat, R. / Kontaxis, G. / Skern, T.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Investigating the Substrate Specificity and Oligomerisation of the Leader Protease of Foot and Mouth Disease Virus using NMR
Authors: Cencic, R. / Mayer, C. / Juliano, M.A. / Juliano, L. / Konrat, R. / Kontaxis, G. / Skern, T.
History
DepositionJun 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Dec 20, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.deposit_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: Genome polyprotein
S: Genome polyprotein


Theoretical massNumber of molelcules
Total (without water)39,5582
Polymers39,5582
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1closest to the average

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Components

#1: Protein Genome polyprotein


Mass: 19779.221 Da / Num. of mol.: 2 / Fragment: residues 29-201 / Mutation: C51A, M126V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Foot-and-mouth disease virus (strain O1)
Genus: Aphthovirus / Species: Foot-and-mouth disease virus / Strain: O1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): (DE)pLysS / References: UniProt: P03305

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HNCO
1313D HNCA
1413D HN(CO)CA
1513D CBCA(CO)NH
1613D HN(CA)CB
1722D 1H-15N IPAP HSQC
1832D 1H-15N IPAP HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-100% 13C; U-100% 15N] Leader Protease, 5 mM DTT, 20 mM sodium phosphate, 50 mM sodium chloride, 10 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 15N] Leader Protease, 5 mM DTT, 20 mM sodium phosphate, 50 mM sodium chloride, 10 mM sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
31 mM [U-100% 15N] Leader Protease, 5 mM DTT, 20 mM sodium phosphate, 50 mM sodium chloride, 10 mM sodium azide, 17 mg/mL Pf1 phage, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMLeader Protease[U-100% 13C; U-100% 15N]1
5 mMDTT1
20 mMsodium phosphate1
50 mMsodium chloride1
10 mMsodium azide1
1 mMLeader Protease[U-100% 15N]2
5 mMDTT2
20 mMsodium phosphate2
50 mMsodium chloride2
10 mMsodium azide2
1 mMLeader Protease[U-100% 15N]3
5 mMDTT3
20 mMsodium phosphate3
50 mMsodium chloride3
10 mMsodium azide3
17 mg/mLPf1 phage3
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA8002
Varian Direct DriveVarianDirect Drive6003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxpeak picking
SparkyGoddardchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: Rigid body refinement of dimeric X-ray crystal structure PDB ID code 1qol against residual dipolar couplings and radius of gyration restraint
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10

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