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- EMDB-45298: Structure of endogenous asymmetric DPYSL2 from rat model of Alzhe... -

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Basic information

Entry
Database: EMDB / ID: EMD-45298
TitleStructure of endogenous asymmetric DPYSL2 from rat model of Alzheimer's disease
Map dataMain Sharpened Map
Sample
  • Tissue: Dihydropyrimidinase-related protein 2
    • Protein or peptide: Dihydropyrimidinase-related protein 2
  • Ligand: GLYCINE
KeywordsDihydropyrimidinase-related protein 2 / NEUROPEPTIDE
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 / Schaffer collateral - CA1 synapse / endocytosis / terminal bouton / myelin sheath / presynapse / growth cone / microtubule / cell differentiation / postsynaptic density / response to xenobiotic stimulus / axon / neuronal cell body / dendrite / synapse / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKhalili Samani E / Keszei AFA / Mazhab-Jafari MT
Funding support Canada, 1 items
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 12, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJan 15, 2025-
Current statusJan 15, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45298.png

Downloads & links

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Map

FileDownload / File: emd_45298.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain Sharpened Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 200 pix.
= 206. Å		1.03 Å/pix.
x 200 pix.
= 206. Å		1.03 Å/pix.
x 200 pix.
= 206. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.088
Minimum - Maximum-0.72099036 - 1.057428
Average (Standard dev.)0.0012005582 (±0.035947632)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 206.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_45298_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_45298_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dihydropyrimidinase-related protein 2

EntireName: Dihydropyrimidinase-related protein 2
Components
  • Tissue: Dihydropyrimidinase-related protein 2
    • Protein or peptide: Dihydropyrimidinase-related protein 2
  • Ligand: GLYCINE

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Supramolecule #1: Dihydropyrimidinase-related protein 2

SupramoleculeName: Dihydropyrimidinase-related protein 2 / type: tissue / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Rattus norvegicus (Norway rat) / Strain: TgF344 / Organ: Brain

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Macromolecule #1: Dihydropyrimidinase-related protein 2

MacromoleculeName: Dihydropyrimidinase-related protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 62.349352 KDa
SequenceString: MSYQGKKNIP RITSDRLLIK GGKIVNDDQS FYADIYMEDG LIKQIGENLI VPGGVKTIEA HSRMVIPGGI DVHTRFQMPD QGMTSADDF FQGTKAALAG GTTMIIDHVV PEPGTSLLAA FDQWREWADS KSCCDYSLHV DITEWHKGIQ EEMEALVKDH G VNSFLVYM ...String:
MSYQGKKNIP RITSDRLLIK GGKIVNDDQS FYADIYMEDG LIKQIGENLI VPGGVKTIEA HSRMVIPGGI DVHTRFQMPD QGMTSADDF FQGTKAALAG GTTMIIDHVV PEPGTSLLAA FDQWREWADS KSCCDYSLHV DITEWHKGIQ EEMEALVKDH G VNSFLVYM AFKDRFQLTD SQIYEVLSVI RDIGAIAQVH AENGDIIAEE QQRILDLGIT GPEGHVLSRP EEVEAEAVNR SI TIANQTN CPLYVTKVMS KSAAEVIAQA RKKGTVVYGE PITASLGTDG SHYWSKNWAK AAAFVTSPPL SPDPTTPDFL NSL LSCGDL QVTGSAHCTF NTAQKAVGKD NFTLIPEGTN GTEERMSVIW DKAVVTGKMD ENQFVAVTST NAAKVFNLYP RKGR ISVGS DADLVIWDPD SVKTISAKTH NSALEYNIFE GMECRGSPLV VISQGKIVLE DGTLHVTEGS GRYIPRKPFP DFVYK RIKA RSRLAELRGV PRGLYDGPVC EVSVTPKTVT PASSAKTSPA KQQAPPVRNL HQSGFSLSGA QIDDNIPRRT TQRIVA PPG GRANITSLG

UniProtKB: Dihydropyrimidinase-related protein 2

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Macromolecule #2: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: GLY
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Homemade / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 3
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV
DetailsCytosolic fraction of rat brain

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE / Details: Ab initio reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 389444
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelChain - Source name: SwissModel / Chain - Initial model type: in silico model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9c86:
Structure of endogenous asymmetric DPYSL2 from rat model of Alzheimer's disease

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