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- PDB-9c4e: Structure of endogenous DPYSL2 from rat model of Alzheimer's disease -

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Basic information

Entry
Database: PDB / ID: 9c4e
TitleStructure of endogenous DPYSL2 from rat model of Alzheimer's disease
ComponentsDihydropyrimidinase-related protein 2
KeywordsNEUROPEPTIDE / Dihydropyrimidinase-related protein 2
Function / homology
Function and homology information


CRMPs in Sema3A signaling / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / Recycling pathway of L1 / olfactory bulb development / positive regulation of glutamate secretion / regulation of neuron differentiation / regulation of axon extension / synaptic vesicle transport / spinal cord development / regulation of neuron projection development ...CRMPs in Sema3A signaling / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / Recycling pathway of L1 / olfactory bulb development / positive regulation of glutamate secretion / regulation of neuron differentiation / regulation of axon extension / synaptic vesicle transport / spinal cord development / regulation of neuron projection development / regulation of postsynapse assembly / cytoskeleton organization / response to amphetamine / response to cocaine / terminal bouton / Schaffer collateral - CA1 synapse / endocytosis / myelin sheath / presynapse / growth cone / microtubule / cell differentiation / postsynaptic density / response to xenobiotic stimulus / axon / neuronal cell body / synapse / dendrite / protein kinase binding / glutamatergic synapse / protein-containing complex / identical protein binding / membrane / cytosol
Similarity search - Function
Hydantoinase/dihydropyrimidinase / : / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
Dihydropyrimidinase-related protein 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsKhalili Samani, E. / Keszei, A.F.A. / Mazhab-Jafari, M.T.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)419240 Canada
CitationJournal: Structure / Year: 2025
Title: Unveiling the structural proteome of an Alzheimer's disease rat brain model.
Authors: Elnaz Khalili Samani / S M Naimul Hasan / Matthew Waas / Alexander F A Keszei / Xiaoxiao Xu / Mahtab Heydari / Mary Elizabeth Hill / JoAnne McLaurin / Thomas Kislinger / Mohammad T Mazhab-Jafari /
Abstract: Studying native protein structures at near-atomic resolution in a crowded environment presents challenges. Consequently, understanding the structural intricacies of proteins within pathologically ...Studying native protein structures at near-atomic resolution in a crowded environment presents challenges. Consequently, understanding the structural intricacies of proteins within pathologically affected tissues often relies on mass spectrometry and proteomic analysis. Here, we utilized cryoelectron microscopy (cryo-EM) and the Build and Retrieve (BaR) method to investigate protein complexes' structural characteristics such as post-translational modification, active site occupancy, and arrested conformational state in Alzheimer's disease (AD) using brain lysate from a rat model (TgF344-AD). Our findings reveal novel insights into the architecture of these complexes, corroborated through mass spectrometry analysis. Interestingly, it has been shown that the dysfunction of these protein complexes extends beyond AD, implicating them in cancer, as well as other neurodegenerative disorders such as Parkinson's disease, Huntington's disease, and schizophrenia. By elucidating these structural details, our work not only enhances our understanding of disease pathology but also suggests new avenues for future approaches in therapeutic intervention.
History
DepositionJun 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydropyrimidinase-related protein 2
B: Dihydropyrimidinase-related protein 2
C: Dihydropyrimidinase-related protein 2
D: Dihydropyrimidinase-related protein 2


Theoretical massNumber of molelcules
Total (without water)249,3974
Polymers249,3974
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Dihydropyrimidinase-related protein 2 / DRP-2 / Collapsin response mediator protein 2 / CRMP-2 / Turned on after division 64 kDa protein / TOAD-64


Mass: 62349.352 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P47942
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Dihydropyrimidinase-related protein 2 / Type: TISSUE / Entity ID: all / Source: NATURAL
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: TgF344 / Organ: Brain
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Cytosolic fraction of rat brain
Specimen supportGrid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2EPUimage acquisition
4cryoSPARC4CTF correction
7Coot9model fitting
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 389444 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingSource name: SwissModel / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00215064
ELECTRON MICROSCOPYf_angle_d0.50220464
ELECTRON MICROSCOPYf_dihedral_angle_d3.8662056
ELECTRON MICROSCOPYf_chiral_restr0.0422324
ELECTRON MICROSCOPYf_plane_restr0.0032668

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