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- PDB-6tub: Beta-endorphin amyloid fibril -

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Basic information

Entry
Database: PDB / ID: 6tub
TitleBeta-endorphin amyloid fibril
ComponentsBeta-endorphin
KeywordsHORMONE / amyloid fibril functional amyloid hormone storage hormone release
Function / homology
Function and homology information


cellular pigmentation / positive regulation of oxytocin production / Peptide hormone biosynthesis / Defective ACTH causes obesity and POMCD / type 1 melanocortin receptor binding / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / regulation of corticosterone secretion / response to melanocyte-stimulating hormone / Opioid Signalling ...cellular pigmentation / positive regulation of oxytocin production / Peptide hormone biosynthesis / Defective ACTH causes obesity and POMCD / type 1 melanocortin receptor binding / type 3 melanocortin receptor binding / type 4 melanocortin receptor binding / regulation of corticosterone secretion / response to melanocyte-stimulating hormone / Opioid Signalling / Androgen biosynthesis / regulation of appetite / regulation of glycogen metabolic process / Glucocorticoid biosynthesis / positive regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of tumor necrosis factor production / neuropeptide signaling pathway / Endogenous sterols / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transcriptional and post-translational regulation of MITF-M expression and activity / Peptide ligand-binding receptors / secretory granule / generation of precursor metabolites and energy / G protein-coupled receptor binding / calcium-mediated signaling / hormone activity / G-protein activation / regulation of blood pressure / cell-cell signaling / glucose homeostasis / G alpha (i) signalling events / G alpha (s) signalling events / Interleukin-4 and Interleukin-13 signaling / secretory granule lumen / signaling receptor binding / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Opiodes neuropeptide / Pro-opiomelanocortin N-terminal / Opioids neuropeptide / Pro-opiomelanocortin, N-terminal region / Pro-opiomelanocortin, N-terminal region / Opioids neuropeptide / Pro-opiomelanocortin / Pro-opiomelanocortin/corticotropin, ACTH, central region / : / Corticotropin ACTH domain / Corticotropin ACTH domain
Similarity search - Domain/homology
Pro-opiomelanocortin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsVerasdonck, J. / Seuring, C. / Gath, J. / Ghosh, D. / Nespovitaya, N. / Waelti, M.A. / Maji, S. / Cadalbert, R. / Boeckmann, A. / Guentert, P. ...Verasdonck, J. / Seuring, C. / Gath, J. / Ghosh, D. / Nespovitaya, N. / Waelti, M.A. / Maji, S. / Cadalbert, R. / Boeckmann, A. / Guentert, P. / Meier, B.H. / Riek, R.
Citation
Journal: Nat.Struct.Mol.Biol. / Year: 2020
Title: The three-dimensional structure of human beta-endorphin amyloid fibrils.
Authors: Seuring, C. / Verasdonck, J. / Gath, J. / Ghosh, D. / Nespovitaya, N. / Walti, M.A. / Maji, S.K. / Cadalbert, R. / Guntert, P. / Meier, B.H. / Riek, R.
#1: Journal: Biomol NMR Assign / Year: 2016
Title: Solid-state NMR sequential assignment of the beta-endorphin peptide in its amyloid form.
Authors: Seuring, C. / Gath, J. / Verasdonck, J. / Cadalbert, R. / Rivier, J. / Boeckmann, A. / Meier, B.H. / Riek, R.
History
DepositionJan 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-endorphin
B: Beta-endorphin
C: Beta-endorphin
D: Beta-endorphin
E: Beta-endorphin
F: Beta-endorphin


Theoretical massNumber of molelcules
Total (without water)20,8206
Polymers20,8206
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: scanning transmission electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area13600 Å2
ΔGint-89 kcal/mol
Surface area8480 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 95target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide
Beta-endorphin


Mass: 3470.022 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POMC / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): STAR / References: UniProt: P01189

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D CHHC
121isotropic12D PAR
131isotropic12D PDSD

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Sample preparation

DetailsType: fiber
Contents: 2 mg/mL [U-100% 13C; U-100% 15N] beta-endorphin, 90 % H2O, 10 % [U-2H] D2O, 90% H2O/10% D2O
Label: uniformly 13C,15N-labeled / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mg/mLbeta-endorphin[U-100% 13C; U-100% 15N]1
90 %H2Onatural abundance1
10 %D2O[U-2H]1
Sample conditionsIonic strength: n.a. Not defined / Label: conditions_1 / pH: 5.5 / Pressure: AMBIENT Pa / Temperature: 273 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz / Details: 3.2 mm triple-resonance "E-free" probe

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.98.3Guentert, P.structure calculation
CcpNmr AnalysisCCPNchemical shift assignment
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 95 / Conformers submitted total number: 10

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