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- PDB-8boo: Spatials structure of amyloidogenic SEM1(45-67) peptide -

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Basic information

Entry
Database: PDB / ID: 8boo
TitleSpatials structure of amyloidogenic SEM1(45-67) peptide
ComponentsSemenogelin-1
KeywordsSTRUCTURAL PROTEIN / HIV / Semenogelin 1 / SEM1 / SEMG1 / SEM1(45-67) / N-terminus of SEM1(45-67) / 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 / extracellular exosome / zinc ion binding / extracellular region / nucleus
Similarity search - Function
Semenogelin / Semenogelin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsBlokhin, D.S. / Osetrina, D.A.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation20-73-10034 Russian Federation
CitationJournal: To Be Published
Title: Spatials structure of amyloidogenic SEM1(45-67) peptide
Authors: Blokhin, D.S. / Osetrina, D.A.
History
DepositionNov 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Semenogelin-1


Theoretical massNumber of molelcules
Total (without water)2,5781
Polymers2,5781
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)11 / 1000structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein/peptide Semenogelin-1 / Cancer/testis antigen 103 / Semenogelin I / SGI


Mass: 2577.761 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
111isotropic12D 1H-1H TOCSY
121isotropic12D 1H-1H NOESY
131isotropic12D 1H-15N HSQC
141isotropic12D 1H-13C HSQC
151isotropic12D 1H-13C HMBC

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Sample preparation

DetailsType: solution
Contents: 0.8 mM GLY-GLN-HIS-TYR-SER-GLY-GLN-LYS-GLY-LYS-GLN-GLN-THR-GLU-SER-LYS-GLY-SER-PHE-SER-ILE-GLN-TYR, 90% H2O/10% D2O
Label: Sample1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.8 mM
Component: GLY-GLN-HIS-TYR-SER-GLY-GLN-LYS-GLY-LYS-GLN-GLN-THR-GLU-SER-LYS-GLY-SER-PHE-SER-ILE-GLN-TYR
Isotopic labeling: natural abundance
Sample conditionsIonic strength: 0 mM / Label: conditions_1 / pH: 3.1 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III HD / Manufacturer: Bruker / Model: AVANCE III HD / Field strength: 700 MHz

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 1000 / Conformers submitted total number: 11

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