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- PDB-4bxl: Structure of alpha-synuclein in complex with an engineered bindin... -

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Basic information

Entry
Database: PDB / ID: 4bxl
TitleStructure of alpha-synuclein in complex with an engineered binding protein
Components
  • ALPHA SYNUCLEIN
  • AS69
KeywordsFIBRIL / AMYLOID / PARKINSON'S DISEASE / PROTEIN AGGREGATION / PROTEIN ENGINEERING / PROTEIN MISFOLDING / SCAFFOLD PROTEINS
Function / homology
Function and homology information


negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber ...negative regulation of mitochondrial electron transport, NADH to ubiquinone / : / neutral lipid metabolic process / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / response to desipramine / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / regulation of synaptic vesicle recycling / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / negative regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of protein localization to cell periphery / negative regulation of exocytosis / regulation of glutamate secretion / dopamine biosynthetic process / SNARE complex assembly / regulation of norepinephrine uptake / response to iron(II) ion / positive regulation of neurotransmitter secretion / positive regulation of inositol phosphate biosynthetic process / regulation of locomotion / negative regulation of dopamine metabolic process / regulation of macrophage activation / transporter regulator activity / negative regulation of microtubule polymerization / synaptic vesicle transport / synaptic vesicle priming / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / mitochondrial ATP synthesis coupled electron transport / regulation of dopamine secretion / dynein complex binding / positive regulation of receptor recycling / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / nuclear outer membrane / response to magnesium ion / positive regulation of endocytosis / positive regulation of exocytosis / synaptic vesicle exocytosis / kinesin binding / enzyme inhibitor activity / synaptic vesicle endocytosis / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / response to type II interferon / regulation of presynapse assembly / alpha-tubulin binding / beta-tubulin binding / behavioral response to cocaine / phospholipase binding / supramolecular fiber organization / phospholipid metabolic process / cellular response to fibroblast growth factor stimulus / inclusion body / axon terminus / Hsp70 protein binding / cellular response to epinephrine stimulus / response to interleukin-1 / regulation of microtubule cytoskeleton organization / cellular response to copper ion / positive regulation of release of sequestered calcium ion into cytosol / SNARE binding / adult locomotory behavior / excitatory postsynaptic potential / phosphoprotein binding / protein tetramerization / microglial cell activation / fatty acid metabolic process / ferrous iron binding / regulation of long-term neuronal synaptic plasticity / synapse organization / protein destabilization / PKR-mediated signaling / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / terminal bouton / positive regulation of inflammatory response / synaptic vesicle membrane / actin cytoskeleton / actin binding / growth cone / cellular response to oxidative stress / neuron apoptotic process / cell cortex / histone binding / response to lipopolysaccharide / microtubule binding / molecular adaptor activity / chemical synaptic transmission / amyloid fibril formation / mitochondrial outer membrane / negative regulation of neuron apoptotic process / oxidoreductase activity
Similarity search - Function
Immunoglobulin FC, subunit C / Synuclein / Alpha-synuclein / Synuclein / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSYNTHETIC CONSTRUCT (others)
HOMO SAPIENS (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMirecka, E.A. / Shaykhalishahi, H. / Lecher, J. / Stoldt, M. / Hoyer, W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Sequestration of a Beta-Hairpin for Control of Alpha-Synuclein Aggregation.
Authors: Mirecka, E.A. / Shaykhalishahi, H. / Gauhar, A. / Akgul, S. / Lecher, J. / Willbold, D. / Stoldt, M. / Hoyer, W.
History
DepositionJul 12, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_cs / _pdbx_database_status.status_code_mr / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AS69
B: AS69
C: ALPHA SYNUCLEIN


Theoretical massNumber of molelcules
Total (without water)12,3813
Polymers12,3813
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100LOWEST ENERGY
RepresentativeModel #5

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Components

#1: Protein/peptide AS69


Mass: 5088.595 Da / Num. of mol.: 2 / Fragment: ENGINEERED BINDING PROTEIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: CHAMPION PET302 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
#2: Protein/peptide ALPHA SYNUCLEIN / NON-A BETA COMPONENT OF AD AMYLOID / NON-A4 COMPONENT OF AMYLOID PRECURSOR / NACP / ALPHA SYNUCLEIN


Mass: 2203.514 Da / Num. of mol.: 1 / Fragment: RESIDUES 35-56
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PT7-7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37840
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: CNSYN AS69 2DNOESY CNDECSTRIP
NMR detailsText: STRUCTURES CREATED BY ARIA2, AS69 RUN31, WATER REFINEMENT.

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Sample preparation

Details
Solution-IDContents
193% H2O/7% D2O
293% H2O/7% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.077.41.0 atm303.0 K
20.077.41.0 atm303.0 K

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NMR measurement

NMR spectrometerType: Varian VNMRS / Manufacturer: Varian / Model: VNMRS / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,READ, RICE,SIMONSON,WARRENrefinement
ARIA2.3.2structure solution
NMRPipe2013.021.23.09structure solution
TALOS+3.80F1.2012.080.14.41structure solution
CcpNmr Analysis2.2structure solution
VnmrJ2.3Astructure solution
CcpNmr Analysis2.3structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 100 / Conformers submitted total number: 10

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