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- EMDB-26353: Cryo-EM Structure of DPYSL2 -

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Basic information

Entry
Database: EMDB / ID: EMD-26353
TitleCryo-EM Structure of DPYSL2
Map dataDensity-modified map of DPYSL2 from bos taurus
Sample
  • Complex: Homo-tetramer of DPYSL2
    • Protein or peptide: Dihydropyrimidinase-related protein 2
  • Ligand: water
KeywordsDPYSL2 / dihydropyrimidinase-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 / cytoskeleton organization / endocytosis / nervous system development / cell differentiation / cytoskeleton / 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 speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.78 Å
AuthorsMorgan CE / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell Rep / Year: 2022
Title: Toward structural-omics of the bovine retinal pigment epithelium.
Authors: Christopher E Morgan / Zhemin Zhang / Masaru Miyagi / Marcin Golczak / Edward W Yu /
Abstract: The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on ...The use of an integrated systems biology approach to investigate tissues and organs has been thought to be impracticable in the field of structural biology, where the techniques mainly focus on determining the structure of a particular biomacromolecule of interest. Here, we report the use of cryoelectron microscopy (cryo-EM) to define the composition of a raw bovine retinal pigment epithelium (RPE) lysate. From this sample, we simultaneously identify and solve cryo-EM structures of seven different RPE enzymes whose functions affect neurotransmitter recycling, iron metabolism, gluconeogenesis, glycolysis, axonal development, and energy homeostasis. Interestingly, dysfunction of these important proteins has been directly linked to several neurodegenerative disorders, including Huntington's disease, amyotrophic lateral sclerosis (ALS), Parkinson's disease, Alzheimer's disease, and schizophrenia. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
History
DepositionMar 2, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26353.png

Downloads & links

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Map

FileDownload / File: emd_26353.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDensity-modified map of DPYSL2 from bos taurus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.4130325 - 3.2887628
Average (Standard dev.)0.000020514666 (±0.086685754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of DPYSL2 from bos taurus

Fileemd_26353_additional_1.map
AnnotationUnsharpened map of DPYSL2 from bos taurus
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A

Fileemd_26353_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_26353_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 : Homo-tetramer of DPYSL2

EntireName: Homo-tetramer of DPYSL2
Components
  • Complex: Homo-tetramer of DPYSL2
    • Protein or peptide: Dihydropyrimidinase-related protein 2
  • Ligand: water

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Supramolecule #1: Homo-tetramer of DPYSL2

SupramoleculeName: Homo-tetramer of DPYSL2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle)

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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: Bos taurus (cattle)
Molecular weightTheoretical: 62.349352 KDa
SequenceString: MSYQGKKNIP RITSDRLLIK GGKIVNDDQS FYADIYMEDG LIKQIGENLI VPGGVKTIEA HSRMVIPGGI DVHTRFQMPD QGMTSADDF FQGTKAALAG GTTMIIDHVV PEPGTSLLAA FDQWREWADS KSCCDYSLHV DITEWHKGVQ EEMEALVKDH G VNSFLVYM ...String:
MSYQGKKNIP RITSDRLLIK GGKIVNDDQS FYADIYMEDG LIKQIGENLI VPGGVKTIEA HSRMVIPGGI DVHTRFQMPD QGMTSADDF FQGTKAALAG GTTMIIDHVV PEPGTSLLAA FDQWREWADS KSCCDYSLHV DITEWHKGVQ EEMEALVKDH G VNSFLVYM AFKDRFQLTD SQIYEVLSVI RDIGAIAQVH AENGDIIAEE QQRILDLGIT GPEGHVLSRP EEVEAEAVNR SI TIANQTN CPLYITKVMS KSAAEVIAQA RKKGTVVYGE PITASLGTDG SHYWSKNWAK AAAFVTSPPL SPDPTTPDFL NSL LSCGDL QVTGSAHCTF NTAQKAVGKD NFTLIPEGTN GTEERMSVIW DKAVVTGKMD ENQFVAVTST NAAKVFNLYP RKGR IAVGS DADLVIWDPD SVKTISAKTH NSSLEYNIFE 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: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 148 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3) / Number images used: 16491
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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