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- PDB-3q28: Cyrstal structure of human alpha-synuclein (58-79) fused to malto... -

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Basic information

Entry
Database: PDB / ID: 3q28
TitleCyrstal structure of human alpha-synuclein (58-79) 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 / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization ...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 / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of synaptic vesicle recycling / 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 / response to iron(II) ion / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of norepinephrine uptake / transporter regulator activity / regulation of locomotion / synaptic vesicle priming / mitochondrial ATP synthesis coupled electron transport / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / negative regulation of microtubule polymerization / synaptic vesicle transport / positive regulation of receptor recycling / dopamine uptake involved in synaptic transmission / detection of maltose stimulus / protein kinase inhibitor activity / dynein complex binding / maltose transport complex / regulation of dopamine secretion / negative regulation of thrombin-activated receptor signaling pathway / cuprous ion binding / positive regulation of endocytosis / carbohydrate transport / positive regulation of exocytosis / response to magnesium ion / synaptic vesicle exocytosis / enzyme inhibitor activity / kinesin binding / synaptic vesicle endocytosis / response to type II interferon / regulation of presynapse assembly / cysteine-type endopeptidase inhibitor activity / negative regulation of serotonin uptake / carbohydrate transmembrane transporter activity / maltose binding / alpha-tubulin binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / supramolecular fiber organization / inclusion body / phospholipid metabolic process / cellular response to copper ion / axon terminus / cellular response to epinephrine stimulus / Hsp70 protein binding / response to interleukin-1 / regulation of microtubule cytoskeleton organization / ATP-binding cassette (ABC) transporter complex / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / adult locomotory behavior / negative regulation of protein kinase activity / excitatory postsynaptic potential / fatty acid metabolic process / cell chemotaxis / phosphoprotein binding / protein tetramerization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / synapse organization / ferrous iron binding / protein destabilization / PKR-mediated signaling / phospholipid binding / receptor internalization / tau protein binding / long-term synaptic potentiation / synaptic vesicle membrane / positive regulation of inflammatory response / actin cytoskeleton / actin binding / outer membrane-bounded periplasmic space / growth cone / cell cortex / cellular response to oxidative stress / neuron apoptotic process / chemical synaptic transmission / molecular adaptor activity / negative regulation of neuron apoptotic process / response to lipopolysaccharide / histone binding
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: 1.6 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 1.3Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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 / 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_atom_id / _atom_site.label_comp_id / _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_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6276
Polymers42,9001
Non-polymers7275
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.540, 48.570, 57.850
Angle α, β, γ (deg.)90.000, 94.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 42900.461 Da / Num. of mol.: 1
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.: 1
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 1.88 Å3/Da / Density % sol: 34.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M BICINE pH 9.0, 3.2 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: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.6→19.632 Å / Num. obs: 42173 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.459 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 22.74
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.6-1.640.5574329693091100
1.64-1.690.4965.240013302899.9
1.69-1.740.3986.840887293799.9
1.74-1.790.3248.2400352858100
1.79-1.850.26310.1385852752100
1.85-1.910.21212.537587269199.9
1.91-1.980.15616.436439261699.9
1.98-2.070.12820.4344692466100
2.07-2.160.10624.1337102403100
2.16-2.260.09427.4315852268100
2.26-2.390.0929.9303102186100
2.39-2.530.08133.128753208199.9
2.53-2.70.07535.6267251951100
2.7-2.920.0739.224609179599.8
2.92-3.20.06442.7226351677100
3.2-3.580.0647201111523100
3.58-4.130.05449.117590134199.8
4.13-5.060.04852.115668113099.8
5.06-7.160.04851.212353897100
7.160.03751.1621748294.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å19.63 Å
Translation2 Å19.63 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: 1.6→19.632 Å / Occupancy max: 1 / Occupancy min: 0.39 / FOM work R set: 0.9048 / SU ML: 0.16 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1728 2109 5 %random
Rwork0.1517 ---
obs0.1527 42171 99.96 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.427 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 77.18 Å2 / Biso mean: 17.5407 Å2 / Biso min: 5.45 Å2
Baniso -1Baniso -2Baniso -3
1--2.6466 Å20 Å20.166 Å2
2--5.5996 Å20 Å2
3----2.953 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2929 0 43 310 3282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083180
X-RAY DIFFRACTIONf_angle_d1.1184357
X-RAY DIFFRACTIONf_chiral_restr0.076491
X-RAY DIFFRACTIONf_plane_restr0.005558
X-RAY DIFFRACTIONf_dihedral_angle_d12.0571186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6-1.63720.2611380.217726232761
1.6372-1.67810.23741410.197326742815
1.6781-1.72350.19691380.17226332771
1.7235-1.77420.22631390.165326342773
1.7742-1.83140.19151400.160626612801
1.8314-1.89680.20861400.161326622802
1.8968-1.97270.20831400.145726662806
1.9727-2.06240.16291420.146826802822
2.0624-2.1710.16561390.147326562795
2.171-2.30680.1611420.144326882830
2.3068-2.48460.1451390.146726462785
2.4846-2.7340.20621410.156326822823
2.734-3.12830.19121420.159827022844
3.1283-3.93610.14341420.136226942836
3.9361-19.6330.14241460.142727612907
Refinement TLS params.Method: refined / Origin x: -9.9416 Å / Origin y: 6.9732 Å / Origin z: -12.8454 Å
111213212223313233
T0.0569 Å2-0.0007 Å20.001 Å2-0.0412 Å2-0.0076 Å2--0.0581 Å2
L0.4442 °20.1789 °20.0039 °2-0.1595 °2-0.091 °2--0.308 °2
S-0.0109 Å °0.0124 Å °0.0106 Å °-0.0042 Å °0.0198 Å °0.0021 Å °0.0133 Å °0.0209 Å °-0.0062 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 386
2X-RAY DIFFRACTION1allA5044
3X-RAY DIFFRACTION1allA5044
4X-RAY DIFFRACTION1allA1 - 707
5X-RAY DIFFRACTION1allA1 - 395
6X-RAY DIFFRACTION1allA3 - 397

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