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- EMDB-27574: Human Brain Dihydropyrimidinase-related protein 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-27574
TitleHuman Brain Dihydropyrimidinase-related protein 2
Map data
Sample
  • Complex: Dihydropyrimdinase-related protein 2
    • Protein or peptide: Dihydropyrimidinase-related protein 2
Keywordshuman brain / DPYSL2 / HYDROLASE
Function / homology
Function and homology information


dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / Recycling pathway of L1 / cytoskeleton organization / endocytosis / mitotic spindle / nervous system development / microtubule cytoskeleton ...dihydropyrimidinase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides / CRMPs in Sema3A signaling / nucleobase-containing compound metabolic process / Recycling pathway of L1 / cytoskeleton organization / endocytosis / mitotic spindle / nervous system development / microtubule cytoskeleton / cell differentiation / cilium / signal transduction / extracellular exosome / identical protein binding / plasma 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.76 Å
AuthorsTringides ML
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Life Sci Alliance / Year: 2023
Title: A cryo-electron microscopic approach to elucidate protein structures from human brain microsomes.
Authors: Marios L Tringides / Zhemin Zhang / Christopher E Morgan / Chih-Chia Su / Edward W Yu /
Abstract: We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual ...We recently developed a "Build and Retrieve" cryo-electron microscopy (cryo-EM) methodology, which is capable of simultaneously producing near-atomic resolution cryo-EM maps for several individual proteins from a heterogeneous, multiprotein sample. Here we report the use of "Build and Retrieve" to define the composition of a raw human brain microsomal lysate. From this sample, we simultaneously identify and solve cryo-EM structures of five different brain enzymes whose functions affect neurotransmitter recycling, iron metabolism, glycolysis, axonal development, energy homeostasis, and retinoic acid biosynthesis. Interestingly, malfunction of these important proteins has been directly linked to several neurodegenerative disorders, such as Alzheimer's, Huntington's, and Parkinson's diseases. Our work underscores the importance of cryo-EM in facilitating tissue and organ proteomics at the atomic level.
History
DepositionJul 11, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27574.png

Downloads & links

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Map

FileDownload / File: emd_27574.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. 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: 0.2
Minimum - Maximum-0.32104656 - 0.78356814
Average (Standard dev.)0.00013232659 (±0.02106259)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27574_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27574_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Dihydropyrimdinase-related protein 2

EntireName: Dihydropyrimdinase-related protein 2
Components
  • Complex: Dihydropyrimdinase-related protein 2
    • Protein or peptide: Dihydropyrimidinase-related protein 2

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Supramolecule #1: Dihydropyrimdinase-related protein 2

SupramoleculeName: Dihydropyrimdinase-related protein 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: Homo sapiens (human)
Molecular weightTheoretical: 62.365414 KDa
SequenceString: MSYQGKKNIP RITSDRLLIK GGKIVNDDQS FYADIYMEDG LIKQIGENLI VPGGVKTIEA HSRMVIPGGI DVHTRFQMPD QGMTSADDF FQGTKAALAG GTTMIIDHVV PEPGTSLLAA FDQWREWADS KSCCDYSLHV DISEWHKGIQ EEMEALVKDH G VNSFLVYM ...String:
MSYQGKKNIP RITSDRLLIK GGKIVNDDQS FYADIYMEDG LIKQIGENLI VPGGVKTIEA HSRMVIPGGI DVHTRFQMPD QGMTSADDF FQGTKAALAG GTTMIIDHVV PEPGTSLLAA FDQWREWADS KSCCDYSLHV DISEWHKGIQ EEMEALVKDH G VNSFLVYM AFKDRFQLTD CQIYEVLSVI RDIGAIAQVH AENGDIIAEE QQRILDLGIT GPEGHVLSRP EEVEAEAVNR AI TIANQTN CPLYITKVMS KSSAEVIAQA 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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statetissue

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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 BIOQUANTUM (6k x 4k) / Average electron dose: 35.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6580000000000001 µm / Nominal defocus min: 0.216 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5mkv

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109192
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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