+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27574 | |||||||||
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Title | Human Brain Dihydropyrimidinase-related protein 2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | human 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 / nervous system development / cell differentiation / 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 / nervous system development / cell differentiation / cytoskeleton / signal transduction / extracellular exosome / identical protein binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.76 Å | |||||||||
Authors | Tringides ML | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27574.map.gz | 93.5 MB | EMDB map data format | |
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Header (meta data) | emd-27574-v30.xml emd-27574.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_27574.png | 70.1 KB | ||
Filedesc metadata | emd-27574.cif.gz | 5.1 KB | ||
Others | emd_27574_half_map_1.map.gz emd_27574_half_map_2.map.gz | 95.2 MB 95.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27574 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27574 | HTTPS FTP |
-Validation report
Summary document | emd_27574_validation.pdf.gz | 974.8 KB | Display | EMDB validaton report |
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Full document | emd_27574_full_validation.pdf.gz | 974.4 KB | Display | |
Data in XML | emd_27574_validation.xml.gz | 13.5 KB | Display | |
Data in CIF | emd_27574_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27574 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27574 | HTTPS FTP |
-Related structure data
Related structure data | 8dnmMC 8dnoC 8dnpC 8dnsC 8dnuC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27574.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_27574_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_27574_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dihydropyrimdinase-related protein 2
Entire | Name: Dihydropyrimdinase-related protein 2 |
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Components |
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-Supramolecule #1: Dihydropyrimdinase-related protein 2
Supramolecule | Name: Dihydropyrimdinase-related protein 2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Dihydropyrimidinase-related protein 2
Macromolecule | Name: Dihydropyrimidinase-related protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 62.365414 KDa |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | tissue |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 35.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109192 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |