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- PDB-3q27: Cyrstal structure of human alpha-synuclein (32-57) fused to malto... -

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Basic information

Entry
Database: PDB / ID: 3q27
TitleCyrstal structure of human alpha-synuclein (32-57) 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: 1.302 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)44,1566
Polymers43,4331
Non-polymers7235
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.511, 49.951, 59.342
Angle α, β, γ (deg.)90.00, 92.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 43433.109 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.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 1.96 Å3/Da / Density % sol: 37.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M bicine pH 9.0, 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: 0.97949 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.3→80 Å / Num. obs: 82058 / % possible obs: 99.6 % / Redundancy: 6.2 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.078 / Χ2: 1.017 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.3-1.355.70.56881810.907199.9
1.35-1.46.10.43381960.9981100
1.4-1.466.20.31482010.9751100
1.46-1.546.20.22481791.0831100
1.54-1.646.30.16682191.0391100
1.64-1.766.30.125821411100
1.76-1.946.30.10482371.0881100
1.94-2.226.40.09482441.093199.9
2.22-2.86.20.0782931.0151100
2.8-806.20.0580940.955196.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.5 Å59.3 Å
Translation1.5 Å59.3 Å

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Processing

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

1anf


Resolution: 1.302→59.299 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.9236 / SU ML: 0.17 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1559 4110 5.01 %random
Rwork0.131 ---
obs0.1323 81995 99.39 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.181 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 54.19 Å2 / Biso mean: 17.5836 Å2 / Biso min: 7.31 Å2
Baniso -1Baniso -2Baniso -3
1--2.1635 Å20 Å26.5607 Å2
2---1.2136 Å20 Å2
3---3.3771 Å2
Refinement stepCycle: LAST / Resolution: 1.302→59.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2969 0 44 471 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073215
X-RAY DIFFRACTIONf_angle_d1.1644406
X-RAY DIFFRACTIONf_chiral_restr0.073499
X-RAY DIFFRACTIONf_plane_restr0.006563
X-RAY DIFFRACTIONf_dihedral_angle_d12.3461190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3016-1.31690.32321250.30682605273096
1.3169-1.33290.28841300.273626502780100
1.3329-1.34980.26841390.229527022841100
1.3498-1.36760.2321530.199726732826100
1.3676-1.38630.21771480.175926972845100
1.3863-1.40610.21991250.160126912816100
1.4061-1.42710.20051540.146826852839100
1.4271-1.44940.18521560.133326422798100
1.4494-1.47320.19161450.114226912836100
1.4732-1.49860.15011320.110126932825100
1.4986-1.52580.15511590.102326822841100
1.5258-1.55520.15541340.098827422876100
1.5552-1.58690.15531380.097326602798100
1.5869-1.62140.13761330.092727052838100
1.6214-1.65910.12221400.092726832823100
1.6591-1.70060.13711430.093626822825100
1.7006-1.74660.13231380.09527032841100
1.7466-1.7980.13641320.095927272859100
1.798-1.85610.13271420.102627192861100
1.8561-1.92240.16411330.103926802813100
1.9224-1.99940.14821510.116826962847100
1.9994-2.09040.16131470.118126742821100
2.0904-2.20060.14091400.12127322872100
2.2006-2.33850.14991580.117626832841100
2.3385-2.5190.16461400.133227292869100
2.519-2.77250.16491390.141927202859100
2.7725-3.17370.14831620.142427052867100
3.1737-3.99840.1291330.127727492882100
3.9984-59.36040.15281410.16572485262689

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