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- PDB-3q25: Crystal structure of human alpha-synuclein (1-19) fused to maltos... -

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Basic information

Entry
Database: PDB / ID: 3q25
TitleCrystal 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: 1.9 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)44,55218
Polymers42,6961
Non-polymers1,85517
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 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)89,10436
Polymers85,3932
Non-polymers3,71134
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area10340 Å2
ΔGint-231 kcal/mol
Surface area30850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.470, 77.470, 172.640
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 42696.395 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)
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.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 3.05 Å3/Da / Density % sol: 59.7 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 2.2 M AMMONIUM SULFATE, 20% (w/v) GLYCEROL, 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-E / Wavelength: 0.97914 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: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.9→37.795 Å / Num. obs: 42116 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 34.333 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 25.26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.950.5574.5244493069100
1.95-20.4325.7237852978100
2-2.060.3237.3232422920100
2.06-2.120.2389.5225442828100
2.12-2.190.19411.5219052755100
2.19-2.270.15813.6212662673100
2.27-2.360.12616.1203042565100
2.36-2.450.10319195842479100
2.45-2.560.0921.5188122392100
2.56-2.690.0726.1180862299100
2.69-2.830.05930.2167422173100
2.83-30.05134.4157632073100
3-3.210.0441.5155061960100
3.21-3.470.03449.2142121817100
3.47-3.80.0354.913189169499.8
3.8-4.250.0285811785153799.5
4.25-4.910.02859.410143136798.6
4.91-6.010.02859.28680116699
6.01-8.50.02758.7643791796.7
8.50.02550.4235645479.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å52.17 Å
Translation2.5 Å52.17 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: 1.9→37.795 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8827 / SU ML: 0.2 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.196 2105 5 %random
Rwork0.1695 ---
obs0.1708 42101 99.52 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.641 Å2 / ksol: 0.377 e/Å3
Displacement parametersBiso max: 131.88 Å2 / Biso mean: 35.917 Å2 / Biso min: 14.46 Å2
Baniso -1Baniso -2Baniso -3
1-2.9058 Å20 Å2-0 Å2
2--2.9058 Å2-0 Å2
3----5.8117 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2971 0 109 279 3359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063174
X-RAY DIFFRACTIONf_angle_d0.9474319
X-RAY DIFFRACTIONf_chiral_restr0.066470
X-RAY DIFFRACTIONf_plane_restr0.004547
X-RAY DIFFRACTIONf_dihedral_angle_d11.5031152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9001-1.94430.25021380.222226292767100
1.9443-1.99290.23261380.205926272765100
1.9929-2.04680.25811380.189526052743100
2.0468-2.1070.22171390.175426512790100
2.107-2.1750.22311390.165426272766100
2.175-2.25280.19621390.172826472786100
2.2528-2.3430.22411390.170126502789100
2.343-2.44960.21921390.175226392778100
2.4496-2.57870.2331410.179726672808100
2.5787-2.74020.22311400.173526612801100
2.7402-2.95170.21351410.180326872828100
2.9517-3.24860.20751420.174926922834100
3.2486-3.71830.15981430.157327202863100
3.7183-4.68330.14321430.13882726286999
4.6833-37.80280.2011460.18152768291495
Refinement TLS params.Method: refined / Origin x: 3.6125 Å / Origin y: 29.495 Å / Origin z: 10.4683 Å
111213212223313233
T0.0521 Å20.0176 Å20.0181 Å2-0.1267 Å2-0.049 Å2--0.0632 Å2
L0.3495 °2-0.0364 °20.2585 °2-0.5623 °20.0716 °2--1.5346 °2
S-0.0009 Å °0.018 Å °0.0343 Å °-0.0154 Å °0.0031 Å °-0.0405 Å °-0.2371 Å °-0.0165 Å °-0.0094 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA3 - 390
2X-RAY DIFFRACTION1allA5044
3X-RAY DIFFRACTION1allA1 - 394
4X-RAY DIFFRACTION1allA8 - 397
5X-RAY DIFFRACTION1allA27 - 398
6X-RAY DIFFRACTION1allA1 - 683
7X-RAY DIFFRACTION1allA1 - 399
8X-RAY DIFFRACTION1allA1 - 400
9X-RAY DIFFRACTION1allA1 - 401
10X-RAY DIFFRACTION1allA1 - 402
11X-RAY DIFFRACTION1allA1 - 403
12X-RAY DIFFRACTION1allA1 - 404

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