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- PDB-4r0w: Vvtgvta, an amyloid forming segment from alpha synuclein, residue... -

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Basic information

Entry
Database: PDB / ID: 4r0w
TitleVvtgvta, an amyloid forming segment from alpha synuclein, residues 70-76
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 / positive regulation of protein localization to cell periphery / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / dopamine biosynthetic process / response to iron(II) ion / SNARE complex assembly / negative regulation of dopamine metabolic process / positive regulation of neurotransmitter secretion / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / regulation of norepinephrine uptake / regulation of locomotion / synaptic vesicle transport / negative regulation of microtubule polymerization / transporter regulator activity / synaptic vesicle priming / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / mitochondrial ATP synthesis coupled electron transport / positive regulation of receptor recycling / dynein complex binding / cuprous ion binding / nuclear outer membrane / response to magnesium ion / positive regulation of exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / kinesin binding / synaptic vesicle endocytosis / enzyme inhibitor activity / cysteine-type endopeptidase inhibitor activity / response to type II interferon / negative regulation of serotonin uptake / regulation of presynapse assembly / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / supramolecular fiber organization / cellular response to fibroblast growth factor stimulus / phospholipid metabolic process / axon terminus / inclusion body / cellular response to epinephrine stimulus / Hsp70 protein binding / 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 / protein tetramerization / phosphoprotein binding / microglial cell activation / ferrous iron binding / fatty acid metabolic process / regulation of long-term neuronal synaptic plasticity / synapse organization / PKR-mediated signaling / protein destabilization / 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 / chemical synaptic transmission / amyloid fibril formation / molecular adaptor activity / negative regulation of neuron apoptotic process / oxidoreductase activity / mitochondrial outer membrane
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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)6461
Polymers6461
Non-polymers00
Water181
1
A: Alpha-synuclein
x 10


Theoretical massNumber of molelcules
Total (without water)6,45710
Polymers6,45710
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 operation4_556-x+1/2,y+1/2,-z+11
crystal symmetry operation4_536-x+1/2,y-3/2,-z+11
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
crystal symmetry operation4_566-x+1/2,y+3/2,-z+11
crystal symmetry operation4_576-x+1/2,y+5/2,-z+11
Unit cell
Length a, b, c (Å)50.367, 4.823, 15.692
Angle α, β, γ (deg.)90.000, 107.890, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

DetailsThe biological unit is a fibril, comprising a pair of 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 1/2-X,1/2+Y,-Z+1 and its unit cell translations along the b direction (i.e. 1/2-X,3/2+Y,-Z+1; 1/2-X,5/2+Y,-Z+1; etc.). REMARK 350 displays 5 strands from each sheet.

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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: 645.745 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 70-76 / Source method: obtained synthetically
Details: VVTGVTA (residues 70-76) 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.: 1 / 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: 1.4 Å3/Da / Density % sol: 12.42 % / Mosaicity: 0.6 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: isopropanol, sodium cacodylate, pH 6.5, 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 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.895432 Å / Relative weight: 1
ReflectionResolution: 1.5→90 Å / Num. all: 650 / Num. obs: 650 / % possible obs: 93.9 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.193 / Χ2: 1.113 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.622.30.1771211.00388.3
1.62-1.782.10.4911061.08185.5
1.78-2.043.40.3771281.13697.7
2.04-2.563.90.2561441.10998.6
2.56-903.50.1641511.15398.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.6 Å23.97 Å
Translation1.6 Å23.97 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.2phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ideal beta strand

Resolution: 1.5→23.97 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.3048 / WRfactor Rwork: 0.274 / FOM work R set: 0.7168 / SU B: 3.234 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1311 / SU Rfree: 0.1219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2739 62 9.6 %RANDOM
Rwork0.244 ---
all0.2467 648 --
obs0.2467 648 93.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 39.73 Å2 / Biso mean: 11.91 Å2 / Biso min: 12.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å20.53 Å2
2---3 Å20 Å2
3---2.95 Å2
Refinement stepCycle: LAST / Resolution: 1.5→23.97 Å /
ProteinNucleic acidLigandSolventTotal
Num. atoms45 0 0 1 46
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02344
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.98461
X-RAY DIFFRACTIONr_angle_other_deg0.873350
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg6.614155
X-RAY DIFFRACTIONr_chiral_restr0.0870.211
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0246
X-RAY DIFFRACTIONr_gen_planes_other00.026
X-RAY DIFFRACTIONr_nbd_refined0.0640.22
X-RAY DIFFRACTIONr_nbd_other0.2480.215
X-RAY DIFFRACTIONr_nbtor_refined0.170.224
X-RAY DIFFRACTIONr_nbtor_other0.0970.226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.070.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2130.27
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.21
X-RAY DIFFRACTIONr_mcbond_it2.408241
X-RAY DIFFRACTIONr_mcbond_other0.371214
X-RAY DIFFRACTIONr_mcangle_it2.981356
X-RAY DIFFRACTIONr_scbond_it1.568210
X-RAY DIFFRACTIONr_scangle_it1.12435
LS refinement shellResolution: 1.502→1.678 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.405 22 -
Rwork0.37 143 -
all-165 -
obs--85.94 %

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