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- PDB-5crw: Crystal structure of the b'-a' domain of oxidized protein disulfi... -

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Basic information

Entry
Database: PDB / ID: 5crw
TitleCrystal structure of the b'-a' domain of oxidized protein disulfide isomerase complexed with alpha-synuclein peptide (31-41)
Components
  • Peptide from Alpha-synuclein
  • Protein disulfide-isomerase
KeywordsISOMERASE/METAL BINDING PROTEIN / THIOREDOXIN FOLD / ISOMERASE / DISULFIDE BOND / ENDOPLASMIC RETICULUM / THIOREDOXIN / OXIDOREDUCTASE / ISOMERASE-METAL BINDING PROTEIN complex
Function / homology
Function and homology information


protein disulfide-isomerase / negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly ...protein disulfide-isomerase / negative regulation of mitochondrial electron transport, NADH to ubiquinone / neutral lipid metabolic process / regulation of phospholipase activity / negative regulation of monooxygenase activity / regulation of acyl-CoA biosynthetic process / negative regulation of dopamine uptake involved in synaptic transmission / negative regulation of norepinephrine uptake / positive regulation of glutathione peroxidase activity / positive regulation of SNARE complex assembly / positive regulation of hydrogen peroxide catabolic process / supramolecular fiber / negative regulation of transporter activity / mitochondrial membrane organization / negative regulation of chaperone-mediated autophagy / regulation of reactive oxygen species biosynthetic process / positive regulation of protein localization to cell periphery / regulation of synaptic vesicle recycling / negative regulation of platelet-derived growth factor receptor signaling pathway / negative regulation of exocytosis / regulation of glutamate secretion / regulation of norepinephrine uptake / response to iron(II) ion / SNARE complex assembly / positive regulation of neurotransmitter secretion / dopamine biosynthetic process / regulation of locomotion / positive regulation of inositol phosphate biosynthetic process / synaptic vesicle priming / regulation of macrophage activation / negative regulation of microtubule polymerization / dopamine uptake involved in synaptic transmission / synaptic vesicle transport / dynein complex binding / positive regulation of receptor recycling / regulation of dopamine secretion / protein disulfide isomerase activity / protein kinase inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / response to type II interferon / cuprous ion binding / positive regulation of exocytosis / synaptic vesicle exocytosis / kinesin binding / positive regulation of endocytosis / mitochondrial ATP synthesis coupled electron transport / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / response to magnesium ion / regulation of presynapse assembly / synaptic vesicle endocytosis / negative regulation of serotonin uptake / alpha-tubulin binding / localization / phospholipid metabolic process / supramolecular fiber organization / axon terminus / inclusion body / cellular response to copper ion / Hsp70 protein binding / cellular response to epinephrine stimulus / excitatory postsynaptic potential / response to endoplasmic reticulum stress / response to interleukin-1 / adult locomotory behavior / SNARE binding / positive regulation of release of sequestered calcium ion into cytosol / fatty acid metabolic process / long-term synaptic potentiation / phosphoprotein binding / protein tetramerization / regulation of transmembrane transporter activity / synapse organization / microglial cell activation / regulation of long-term neuronal synaptic plasticity / negative regulation of protein kinase activity / protein destabilization / ferrous iron binding / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / PKR-mediated signaling / tau protein binding / positive regulation of protein serine/threonine kinase activity / receptor internalization / phospholipid binding / synaptic vesicle membrane / positive regulation of inflammatory response / activation of cysteine-type endopeptidase activity involved in apoptotic process / actin cytoskeleton / protein folding / positive regulation of peptidyl-serine phosphorylation / actin binding / cell cortex / histone binding / cellular response to oxidative stress / growth cone / postsynapse / chemical synaptic transmission / neuron apoptotic process / negative regulation of neuron apoptotic process / amyloid fibril formation / response to lipopolysaccharide
Similarity search - Function
Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Synuclein / Alpha-synuclein / Synuclein / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. ...Protein disulphide isomerase / Thioredoxin-like domain / Disulphide isomerase / Synuclein / Alpha-synuclein / Synuclein / Endoplasmic reticulum targeting sequence. / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-synuclein / Alpha-synuclein / Protein disulfide-isomerase
Similarity search - Component
Biological speciesHumicola insolens (fungus)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYagi-Utsumi, M. / Satoh, T. / Kato, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS/MEXT15K21680, 24770102, 25102001, 25102008, 25121730 Japan
CitationJournal: Sci Rep / Year: 2015
Title: Structural basis of redox-dependent substrate binding of protein disulfide isomerase.
Authors: Yagi-Utsumi, M. / Satoh, T. / Kato, K.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Feb 7, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.title / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Protein disulfide-isomerase
B: Peptide from Alpha-synuclein


Theoretical massNumber of molelcules
Total (without water)28,1662
Polymers28,1662
Non-polymers00
Water6,107339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area780 Å2
ΔGint-6 kcal/mol
Surface area13330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.753, 62.510, 68.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Protein disulfide-isomerase / PDI


Mass: 27013.658 Da / Num. of mol.: 1 / Fragment: UNP residues 228-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Humicola insolens (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P55059, protein disulfide-isomerase
#2: Protein/peptide Peptide from Alpha-synuclein


Mass: 1152.341 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: D6RA31, UniProt: P37840*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% (w/v) PEG 3350, 0.1 M HEPES buffer (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 33940 / Num. obs: 32430 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 50
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 10.3 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WT2

3wt2


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.833 / SU ML: 0.065 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1586 5 %RANDOM
Rwork0.184 ---
obs0.185 30166 95.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.54 Å20 Å20 Å2
2---1.85 Å20 Å2
3----0.7 Å2
Refinement stepCycle: 1 / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1960 0 0 339 2299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022004
X-RAY DIFFRACTIONr_bond_other_d0.0010.021931
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9782713
X-RAY DIFFRACTIONr_angle_other_deg0.75734482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0820.2298
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212254
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02410
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8092.431010
X-RAY DIFFRACTIONr_mcbond_other1.8082.4291009
X-RAY DIFFRACTIONr_mcangle_it2.8173.6441259
X-RAY DIFFRACTIONr_mcangle_other2.8153.6441260
X-RAY DIFFRACTIONr_scbond_it2.6792.736994
X-RAY DIFFRACTIONr_scbond_other2.6772.736994
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1283.9641454
X-RAY DIFFRACTIONr_long_range_B_refined5.61126.4191938
X-RAY DIFFRACTIONr_long_range_B_other5.38225.4941756
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 140 -
Rwork0.201 2201 -
obs--97.54 %

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