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- PDB-8bvz: Spatial structure of amyloidogenic SEM1(49-67) peptide -

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Basic information

Entry
Database: PDB / ID: 8bvz
TitleSpatial structure of amyloidogenic SEM1(49-67) peptide
ComponentsAlpha-inhibin-31
KeywordsPROTEIN FIBRIL / Semenogelin1 / SEM1 / amyloid
Function / homology
Function and homology information


coagulation / positive regulation of serine-type endopeptidase activity / negative regulation of flagellated sperm motility / insemination / negative regulation of calcium ion import / sperm capacitation / Antimicrobial peptides / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / killing of cells of another organism ...coagulation / positive regulation of serine-type endopeptidase activity / negative regulation of flagellated sperm motility / insemination / negative regulation of calcium ion import / sperm capacitation / Antimicrobial peptides / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / killing of cells of another organism / Amyloid fiber formation / protein-containing complex / extracellular space / zinc ion binding / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Semenogelin / Semenogelin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / molecular dynamics
AuthorsSemenova, E.A. / Yulmetov, A.R. / Osetrina, D.A. / Blokhin, D.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science FoundationRSF-20-73-10034 Russian Federation
CitationJournal: To Be Published
Title: Spatial structure of amyloidogenic SEM1(49-67) peptide
Authors: Semenova, E.A. / Yulmetov, A.R. / Osetrina, D.A. / Blokhin, D.S.
History
DepositionDec 6, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-inhibin-31


Theoretical massNumber of molelcules
Total (without water)2,0911
Polymers2,0911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Alpha-inhibin-31


Mass: 2091.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P04279

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic22D 1H-15N HSQC
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-1H ROESY
151isotropic12D 1H-13C HSQC
161isotropic12D 1H-13C HMBC

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Sample preparation

DetailsType: solution / Contents: 0.766 mM SEM1(49-67), 95% H2O/5% D2O / Label: SEM1(49-67) / Solvent system: 95% H2O/5% D2O
SampleConc.: 0.766 mM / Component: SEM1(49-67) / Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 3.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II5001
Bruker AVANCE III HDBrukerAVANCE III HD7002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.2Bruker Biospincollection
CcpNmr Analysis3.1CCPNchemical shift assignment
TopSpin3.2Bruker Biospinprocessing
CcpNmr Analysis3.1CCPNpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: molecular dynamics / Software ordinal: 5
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 100 / Conformers submitted total number: 15

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