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- PDB-7zro: The spatial structure of amyloidogenic SEM1(68-107) peptide -

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Basic information

Entry
Database: PDB / ID: 7zro
TitleThe spatial structure of amyloidogenic SEM1(68-107) peptide
ComponentsSemenogelin-1
KeywordsPROTEIN FIBRIL / semenogelin 1 / amyloid fibril of human semen / HIV enhancer
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 / simulated annealing
AuthorsSanchugova, D.A. / Blokhin, D.S.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation20-73-10034 Russian Federation
CitationJournal: To Be Published
Title: The spatial structure of amyloidogenic SEM1(68-107) peptide
Authors: Sanchugova, D.A. / Blokhin, D.S.
History
DepositionMay 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Source and taxonomy / Structure summary / Category: entity / entity_src_gen
Item: _entity.pdbx_description / _entity_src_gen.gene_src_common_name ..._entity.pdbx_description / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.2Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data
Revision 1.3Jun 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: Semenogelin-1


Theoretical massNumber of molelcules
Total (without water)4,6291
Polymers4,6291
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)10 / 50structures with the least restraint violations
RepresentativeModel #1minimized average structure

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Components

#1: Protein/peptide Semenogelin-1


Mass: 4629.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: We obtained the problems with overlap signals of SEM1(68-107) caused by high mobility of disordered fragments. The structure of SEM1(68-107) was determined by combining the results obtained ...Details: We obtained the problems with overlap signals of SEM1(68-107) caused by high mobility of disordered fragments. The structure of SEM1(68-107) was determined by combining the results obtained for the peptide fragments (SEM1(68-85) and SEM1(86-107)).
Source: (gene. exp.) Homo sapiens (human) / Gene: SEMG1, SEMG / Production host: 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
111isotropic13D CBCA(CO)NH
121isotropic13D C(CO)NH
131isotropic13D HNCA
141isotropic13D HNCO
151isotropic13D HN(CA)CO
161isotropic13D HN(CA)CB
171isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution
Contents: 0.3 mM [U-13C; U-15N] SEM1(68-107) peptide, 90% H2O/10% D2O
Label: sample _1 / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.3 mM / Component: SEM1(68-107) peptide / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 0 Not defined / Label: condition_1 / pH: 8.8 / Pressure: 1 atm / Temperature: 278 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger A. T. et.al.refinement
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
TopSpin3.6Bruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 50 / Conformers submitted total number: 10

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