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- PDB-1bcv: SYNTHETIC PEPTIDE CORRESPONDING TO THE MAJOR IMMUNOGEN SITE OF FM... -

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Basic information

Entry
Database: PDB / ID: 1bcv
TitleSYNTHETIC PEPTIDE CORRESPONDING TO THE MAJOR IMMUNOGEN SITE OF FMD VIRUS, NMR, 10 STRUCTURES
ComponentsPEPTIDE CORRESPONDING TO THE MAJOR IMMUNOGEN SITE OF FMD VIRUS
KeywordsSYNTHETIC PEPTIDE / ANTIGENE
Function / homology
Function and homology information


negative regulation of stress granule assembly / : / L-peptidase / modulation by virus of host chromatin organization / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane ...negative regulation of stress granule assembly / : / L-peptidase / modulation by virus of host chromatin organization / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / 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 / host cell cytoplasm / RNA helicase 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 / virion attachment to host cell / structural molecule activity / 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 / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. ...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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
MethodSOLUTION NMR / torsion angle dynamics
AuthorsPetit, M.C. / Benkirane, N. / Guichard, G. / Phan Chan Du, A. / Cung, M.T. / Briand, J.P. / Muller, S.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Solution structure of a retro-inverso peptide analogue mimicking the foot-and-mouth disease virus major antigenic site. Structural basis for its antigenic cross-reactivity with the parent peptide.
Authors: Petit, M.C. / Benkirane, N. / Guichard, G. / Du, A.P. / Marraud, M. / Cung, M.T. / Briand, J.P. / Muller, S.
History
DepositionMay 3, 1998Processing site: BNL
Revision 1.0Nov 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PEPTIDE CORRESPONDING TO THE MAJOR IMMUNOGEN SITE OF FMD VIRUS


Theoretical massNumber of molelcules
Total (without water)1,9721
Polymers1,9721
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 / 50target function
Representative

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Components

#1: Protein/peptide PEPTIDE CORRESPONDING TO THE MAJOR IMMUNOGEN SITE OF FMD VIRUS


Mass: 1972.235 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: G-H LOOP OF THE PROTEIN VP1 / References: UniProt: P03308

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111COSY
121TOCSY
131ROESY
141NOESY

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Sample preparation

DetailsContents: H2O
Sample conditionsIonic strength: 0.1M PHOSPHATE / pH: 5.7 / Pressure: 1 atm / Temperature: 285 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometerType: Bruker DRX400 / Manufacturer: Bruker / Model: DRX400 / Field strength: 400 MHz

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Processing

Software
NameClassification
DYANAmodel building
DYANArefinement
NMR software
NameVersionDeveloperClassification
DYANA1.4GUNTERT,WUTHRICHrefinement
DYANA-1.4structure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1 / Details: RESTRAINED ENERGY REFINEMENT.
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 50 / Conformers submitted total number: 10

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