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- PDB-3q29: Cyrstal structure of human alpha-synuclein (1-19) fused to maltos... -

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Basic information

Entry
Database: PDB / ID: 3q29
TitleCyrstal structure of human alpha-synuclein (1-19) fused to maltose binding protein (MBP)
ComponentsMaltose-binding periplasmic protein/alpha-synuclein chimeric protein
KeywordsSUGAR BINDING PROTEIN / PROTEIN FIBRIL / fusion protein / amyloid
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 / detection of maltose stimulus / dopamine uptake involved in synaptic transmission / maltose transport complex / 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 / carbohydrate transport / cuprous ion binding / nuclear outer membrane / response to magnesium ion / positive regulation of endocytosis / positive regulation of exocytosis / synaptic vesicle exocytosis / kinesin binding / carbohydrate transmembrane transporter activity / synaptic vesicle endocytosis / enzyme inhibitor activity / maltose binding / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / response to type II interferon / maltose transport / regulation of presynapse assembly / maltodextrin transmembrane transport / alpha-tubulin binding / beta-tubulin binding / phospholipase binding / behavioral response to cocaine / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / ATP-binding cassette (ABC) transporter complex / 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 / cell chemotaxis / 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 / outer membrane-bounded periplasmic space / actin binding / growth cone / cellular response to oxidative stress
Similarity search - Function
Synuclein / Alpha-synuclein / Synuclein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 ...Synuclein / Alpha-synuclein / Synuclein / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / Maltose/maltodextrin-binding periplasmic protein / Alpha-synuclein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsZhao, M. / Sawaya, M.R. / Cascio, D. / Eisenberg, D.
CitationJournal: Protein Sci. / Year: 2011
Title: Structures of segments of alpha-synuclein fused to maltose-binding protein suggest intermediate states during amyloid formation
Authors: Zhao, M. / Cascio, D. / Sawaya, M.R. / Eisenberg, D.
History
DepositionDec 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 2, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Maltose-binding periplasmic protein/alpha-synuclein chimeric protein
C: Maltose-binding periplasmic protein/alpha-synuclein chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,50219
Polymers85,3932
Non-polymers2,11017
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-104 kcal/mol
Surface area31080 Å2
MethodPISA
2
C: Maltose-binding periplasmic protein/alpha-synuclein chimeric protein
hetero molecules

A: Maltose-binding periplasmic protein/alpha-synuclein chimeric protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,50219
Polymers85,3932
Non-polymers2,11017
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y+1/2,-z-1/21
Buried area6250 Å2
ΔGint-110 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.390, 117.470, 146.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Maltose-binding periplasmic protein/alpha-synuclein chimeric protein


Mass: 42696.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: SNCA / Plasmid: pMAL-C2X / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AEX9, UniProt: P37840
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.46 Å3/Da / Density % sol: 64.41 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M TRIS pH 8.0, 2.4 M AMMONIUM SULFATE, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97938 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2.3→34.532 Å / Num. obs: 53017 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 50.218 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 16.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.3-2.360.4613.3191393883100
2.36-2.420.3893.918623376299.9
2.42-2.490.3264.618133368399.9
2.49-2.570.2735.417678359599.9
2.57-2.660.2176.917108346899.9
2.66-2.750.1688.516542336099.9
2.75-2.850.13610.1159913252100
2.85-2.970.10812.215337312399.9
2.97-3.10.08715.314745302299.9
3.1-3.250.06818.613958286299.8
3.25-3.430.05622.113229272999.7
3.43-3.640.04825.912485259999.7
3.64-3.890.04428.911640244399.6
3.89-4.20.04131.310792229599.8
4.2-4.60.03933.39751211999.7
4.6-5.140.03734.18861191599.7
5.14-5.940.03634.28201171599.7
5.94-7.270.03435.76869145399.5
7.27-10.290.03336.65068113597.3
10.290.03133.2226260487

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.98 Å
Translation3 Å45.98 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANF

1anf


Resolution: 2.3→34.532 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8066 / SU ML: 0.33 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 2650 5 %random
Rwork0.1926 ---
obs0.1945 53001 99.63 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.075 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso max: 201.19 Å2 / Biso mean: 53.8536 Å2 / Biso min: 21.48 Å2
Baniso -1Baniso -2Baniso -3
1-19.7861 Å2-0 Å2-0 Å2
2---7.9676 Å2-0 Å2
3----11.8185 Å2
Refinement stepCycle: LAST / Resolution: 2.3→34.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5858 0 125 190 6173
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046114
X-RAY DIFFRACTIONf_angle_d0.8378314
X-RAY DIFFRACTIONf_chiral_restr0.056912
X-RAY DIFFRACTIONf_plane_restr0.0031062
X-RAY DIFFRACTIONf_dihedral_angle_d12.6062203
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.34180.34671380.276526212759100
2.3418-2.38690.25781370.248626032740100
2.3869-2.43560.29471390.236726362775100
2.4356-2.48850.28871360.245625972733100
2.4885-2.54640.2861390.250526462785100
2.5464-2.610.33131390.246326362775100
2.61-2.68060.32891370.240726032740100
2.6806-2.75940.28581390.224426462785100
2.7594-2.84840.25831400.229926412781100
2.8484-2.95020.28831380.23526322770100
2.9502-3.06830.29531390.235226352774100
3.0683-3.20780.2751380.231926272765100
3.2078-3.37680.26511400.227126602800100
3.3768-3.58820.26981410.207926802821100
3.5882-3.86490.21561390.180526482787100
3.8649-4.25320.19941420.15326922834100
4.2532-4.86710.15011410.13126812822100
4.8671-6.12650.18521430.153527112854100
6.1265-34.53570.18561450.16912756290196
Refinement TLS params.Method: refined / Origin x: 20.5368 Å / Origin y: -11.0284 Å / Origin z: -42.0096 Å
111213212223313233
T0.2579 Å20.0052 Å20.0318 Å2-0.2688 Å20.0688 Å2--0.295 Å2
L-0.1274 °20.1142 °2-0.293 °2-0.2574 °2-0.3147 °2--0.6862 °2
S0.0148 Å °0.0042 Å °0.058 Å °-0.0121 Å °0.0117 Å °0.0669 Å °0.059 Å °-0.0037 Å °-0.0223 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 382
2X-RAY DIFFRACTION1allA5044
3X-RAY DIFFRACTION1allC2 - 385
4X-RAY DIFFRACTION1allC5044
5X-RAY DIFFRACTION1allC - A1 - 491
6X-RAY DIFFRACTION1allC - A1 - 392
7X-RAY DIFFRACTION1allC5 - 392
8X-RAY DIFFRACTION1allC - A6 - 394
9X-RAY DIFFRACTION1allA11 - 395
10X-RAY DIFFRACTION1allC1 - 396
11X-RAY DIFFRACTION1allA1
12X-RAY DIFFRACTION1allA1 - 396
13X-RAY DIFFRACTION1allC1 - 397

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