+Open data
-Basic information
Entry | Database: PDB / ID: 7u5k | ||||||
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Title | Cryo-EM Structure of DPYSL2 | ||||||
Components | Dihydropyrimidinase-related protein 2 | ||||||
Keywords | NEUROPEPTIDE / DPYSL2 / dihydropyrimidinase-related protein 2 | ||||||
Function / homology | Function and homology information CRMPs in Sema3A signaling / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / regulation of neuron differentiation / regulation of axon extension / cytoskeleton organization / axon guidance / brain development / endocytosis / microtubule binding / cytoskeleton ...CRMPs in Sema3A signaling / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / regulation of neuron differentiation / regulation of axon extension / cytoskeleton organization / axon guidance / brain development / endocytosis / microtubule binding / cytoskeleton / membrane / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.78 Å | ||||||
Authors | Morgan, C.E. / Yu, E.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7u5k.cif.gz | 333.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7u5k.ent.gz | 273.7 KB | Display | PDB format |
PDBx/mmJSON format | 7u5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7u5k_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7u5k_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7u5k_validation.xml.gz | 59.4 KB | Display | |
Data in CIF | 7u5k_validation.cif.gz | 88.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u5/7u5k ftp://data.pdbj.org/pub/pdb/validation_reports/u5/7u5k | HTTPS FTP |
-Related structure data
Related structure data | 26353MC 7u5hC 7u5iC 7u5jC 7u5lC 7u5mC 7u5nC 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: 62349.352 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: O02675 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Homo-tetramer of DPYSL2 / Type: COMPLEX / Entity ID: #1 / Source: NATURAL |
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Source (natural) | Organism: Bos taurus (cattle) |
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: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 37 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19_4080: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: cryoSPARC / Version: v3 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.78 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 16491 / Symmetry type: POINT | ||||||||||||||||||||||||
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