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- PDB-3q26: Cyrstal structure of human alpha-synuclein (10-42) fused to malto... -

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Basic information

Entry
Database: PDB / ID: 3q26
TitleCyrstal structure of human alpha-synuclein (10-42) 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 / positive regulation of neurotransmitter secretion / negative regulation of dopamine metabolic process / regulation of macrophage activation / positive regulation of inositol phosphate biosynthetic process / regulation of norepinephrine uptake / detection of maltose stimulus / negative regulation of microtubule polymerization / regulation of locomotion / synaptic vesicle transport / transporter regulator activity / synaptic vesicle priming / maltose transport complex / dopamine uptake involved in synaptic transmission / protein kinase inhibitor activity / regulation of dopamine secretion / carbohydrate transport / dynein complex binding / mitochondrial ATP synthesis coupled electron transport / 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 exocytosis / synaptic vesicle exocytosis / positive regulation of endocytosis / carbohydrate transmembrane transporter activity / maltose binding / kinesin binding / synaptic vesicle endocytosis / maltose transport / enzyme inhibitor activity / maltodextrin transmembrane transport / 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 / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / 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 / growth cone / actin binding / 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: 1.54 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 / 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.pdbx_synonyms / _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

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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)45,20611
Polymers44,0231
Non-polymers1,18310
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.740, 57.490, 127.230
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: 44022.781 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 2.03 Å3/Da / Density % sol: 39.43 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M tri-lithium citrate, 2.2 M ammonium sulfate, pH 8.0, 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: Oct 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.54→63.615 Å / Num. obs: 53765 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.84 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.72
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.54-1.580.5613.628711391199.9
1.58-1.620.4664.3285403841100
1.62-1.670.3825.227948371899.9
1.67-1.720.2946.8271613590100
1.72-1.780.2467.9268173504100
1.78-1.840.29.8263063414100
1.84-1.910.15812.325554327299.9
1.91-1.990.11815.6247963170100
1.99-2.080.09619.2239593025100
2.08-2.180.08222.2229902918100
2.18-2.30.07524.1220802788100
2.3-2.430.06826.3209642638100
2.43-2.60.06327.9194872472100
2.6-2.810.05830.4181912316100
2.81-3.080.05332.1165922141100
3.08-3.440.04834.9147551946100
3.44-3.980.04636.7127831745100
3.98-4.870.04238.9111881482100
4.87-6.890.04337.987961177100
6.890.03936.84642697100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.1 Å63.62 Å
Translation2.1 Å63.62 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: 1.54→63.615 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.9101 / SU ML: 0.18 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1831 2689 5 %random
Rwork0.1399 ---
obs0.142 53761 99.95 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.039 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 51.76 Å2 / Biso mean: 14.4152 Å2 / Biso min: 4.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.545 Å2-0 Å2-0 Å2
2---1.2357 Å2-0 Å2
3----1.3092 Å2
Refinement stepCycle: LAST / Resolution: 1.54→63.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3007 0 74 388 3469
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093299
X-RAY DIFFRACTIONf_angle_d1.184505
X-RAY DIFFRACTIONf_chiral_restr0.077500
X-RAY DIFFRACTIONf_plane_restr0.005579
X-RAY DIFFRACTIONf_dihedral_angle_d12.9951232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.54-1.5680.26551400.183526582798
1.568-1.59810.24991380.160226182756
1.5981-1.63070.2471400.169126662806
1.6307-1.66620.23231400.154226462786
1.6662-1.7050.19251390.1326482787
1.705-1.74760.20151410.117126732814
1.7476-1.79490.17191390.122526522791
1.7949-1.84770.20731400.113326612801
1.8477-1.90730.18691390.109626442783
1.9073-1.97550.15191410.106626772818
1.9755-2.05460.17061420.112526862828
2.0546-2.14810.17341400.124326672807
2.1481-2.26140.15741410.129226732814
2.2614-2.4030.18631420.135527082850
2.403-2.58860.18251420.141126952837
2.5886-2.84910.18361430.151827092852
2.8491-3.26130.19841440.1627352879
3.2613-4.10890.16051450.138327632908
4.1089-63.66930.16991530.160828933046

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