+Open data
-Basic information
Entry | Database: PDB / ID: 8dnm | ||||||
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Title | Human Brain Dihydropyrimidinase-related protein 2 | ||||||
Components | Dihydropyrimidinase-related protein 2 | ||||||
Keywords | HYDROLASE / human brain / DPYSL2 | ||||||
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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.76 Å | ||||||
Authors | Tringides, M.L. | ||||||
Funding support | United States, 1items
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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
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dnm.cif.gz | 323.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dnm.ent.gz | 265.3 KB | Display | PDB format |
PDBx/mmJSON format | 8dnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/8dnm ftp://data.pdbj.org/pub/pdb/validation_reports/dn/8dnm | HTTPS FTP |
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-Related structure data
Related structure data | 27574MC 8dnoC 8dnpC 8dnsC 8dnuC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 62365.414 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q16555 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: TISSUE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dihydropyrimdinase-related protein 2 / Type: COMPLEX / Entity ID: all / Source: NATURAL |
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Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1658 nm / Nominal defocus min: 216 nm |
Image recording | Electron dose: 35.3 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.76 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 109192 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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