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- PDB-4r0u: Tgvtava, an amyloid forming segment from alpha synuclein, residue... -

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Basic information

Entry
Database: PDB / ID: 4r0u
TitleTgvtava, an amyloid forming segment from alpha synuclein, residues 72-78
ComponentsAlpha-synuclein
KeywordsPROTEIN FIBRIL / amyloid-like protofibril
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 / regulation of synaptic vesicle recycling / negative regulation of chaperone-mediated autophagy / mitochondrial membrane organization / 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 / response to iron(II) ion / SNARE complex assembly / regulation of locomotion / positive regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / positive regulation of inositol phosphate biosynthetic process / regulation of macrophage activation / regulation of norepinephrine uptake / negative regulation of microtubule polymerization / synaptic vesicle transport / transporter regulator activity / 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 / negative regulation of thrombin-activated receptor signaling pathway / positive regulation of receptor recycling / cuprous ion binding / nuclear outer membrane / response to magnesium ion / positive regulation of endocytosis / positive regulation of exocytosis / synaptic vesicle exocytosis / kinesin binding / synaptic vesicle endocytosis / enzyme inhibitor activity / 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 / phospholipase binding / behavioral response to cocaine / 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 / adult locomotory behavior / SNARE binding / excitatory postsynaptic potential / protein tetramerization / phosphoprotein binding / microglial cell activation / ferrous iron binding / fatty acid metabolic process / 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 / response to lipopolysaccharide / histone binding / microtubule binding / molecular adaptor activity / chemical synaptic transmission / amyloid fibril formation / negative regulation of neuron apoptotic process / mitochondrial outer membrane / oxidoreductase activity
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.38 Å
AuthorsIvanova, M.I. / Eisenberg, D.S. / Sawaya, M.R.
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Structure-based design of functional amyloid materials.
Authors: Li, D. / Jones, E.M. / Sawaya, M.R. / Furukawa, H. / Luo, F. / Ivanova, M. / Sievers, S.A. / Wang, W. / Yaghi, O.M. / Liu, C. / Eisenberg, D.S.
History
DepositionAug 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 14, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)6181
Polymers6181
Non-polymers00
Water1267
1
A: Alpha-synuclein
x 10


Theoretical massNumber of molelcules
Total (without water)6,17710
Polymers6,17710
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_535x,y-2,z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation1_575x,y+2,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
crystal symmetry operation2_636-x+1,y-3/2,-z+11
crystal symmetry operation2_646-x+1,y-1/2,-z+11
crystal symmetry operation2_666-x+1,y+3/2,-z+11
crystal symmetry operation2_676-x+1,y+5/2,-z+11
Unit cell
Length a, b, c (Å)15.584, 4.742, 25.806
Angle α, β, γ (deg.)90.000, 98.960, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThere are two choices of the biological unit. The first choice is a pair of indefinitely long beta sheets constructed from chain A and unit cell translations along the b direction (that is, the b direction corresponds to the fiber axis) (i.e. X,Y,Z; X,Y+1,Z; X,Y+2,Z; etc.) together with a symmetry related sheet formed from 1-X,Y+1/2,1-Z and its unit cell translations along the b direction (i.e. 1-x,y+3/2,1-z; 1-x,y+5/2,1-z, etc.). The second choice of biological unit is a pair of beta sheets constructed from chain A and unit cell translations along the b direction (i.e. X,Y,Z; X,Y+1,Z; X,Y+2,Z; etc.) together with a symmetry related sheet formed from -X,1/2+Y,1-Z and its unit cell translations along the b direction (i.e. -x,y+3/2,1-z; -x,y+5/2,1-z; etc.). REMARK 350 displays 5 strands from both sheets for the first choice.

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Components

#1: Protein/peptide Alpha-synuclein / Non-A beta component of AD amyloid / Non-A4 component of amyloid precursor / NACP


Mass: 617.692 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 72-78 / Source method: obtained synthetically
Details: TGVTAVA (residues 72-78) from Human alpha-synuclein, synthesized
Source: (synth.) Homo sapiens (human) / References: UniProt: P37840
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.52 Å3/Da / Density % sol: 19.34 % / Mosaicity: 0.6 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2M magnesium formate, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.895432 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895432 Å / Relative weight: 1
ReflectionResolution: 1.38→90 Å / Num. all: 798 / Num. obs: 798 / % possible obs: 83.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.151 / Χ2: 1.125 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.4-1.511.80.2291151.01761.2
1.51-1.662.40.3291361.10771.2
1.66-1.93.60.2621551.12394.5
1.9-2.394.30.2051971.09196.6
2.39-904.10.131951.18595.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å25.49 Å
Translation1.6 Å25.49 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal beta strand

Resolution: 1.38→25.49 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.967 / WRfactor Rfree: 0.2528 / WRfactor Rwork: 0.2378 / FOM work R set: 0.7067 / SU B: 2.336 / SU ML: 0.077 / SU R Cruickshank DPI: 0.096 / SU Rfree: 0.0873 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 90 11.3 %RANDOM
Rwork0.2027 ---
all0.2045 798 --
obs0.2045 798 86.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 41.77 Å2 / Biso mean: 16.624 Å2 / Biso min: 8.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å2-0 Å20.22 Å2
2---0.21 Å2-0 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.38→25.49 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms43 0 0 7 50
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0242
X-RAY DIFFRACTIONr_bond_other_d0.0020.0245
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.97458
X-RAY DIFFRACTIONr_angle_other_deg0.5443101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.88756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg3.831154
X-RAY DIFFRACTIONr_chiral_restr0.060.210
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0246
X-RAY DIFFRACTIONr_gen_planes_other00.026
X-RAY DIFFRACTIONr_mcbond_it3.6922.02727
X-RAY DIFFRACTIONr_mcbond_other2.3271.91126
X-RAY DIFFRACTIONr_mcangle_it5.8273.25431
LS refinement shellResolution: 1.38→1.542 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.346 19 -
Rwork0.323 163 -
all-182 -
obs--68.94 %

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