+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26350 | |||||||||
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Title | Cryo-EM Structure of DNPEP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNPEP / aminopeptidase / tetrahedral Symmetry / PEPTIDE BINDING PROTEIN | |||||||||
Function / homology | Function and homology information aspartyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / proteolysis / zinc ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.32 Å | |||||||||
Authors | Morgan CE / Yu EW / Zhang Z | |||||||||
Funding support | United States, 1 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26350.map.gz | 14.8 MB | EMDB map data format | |
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Header (meta data) | emd-26350-v30.xml emd-26350.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26350_fsc.xml | 8.4 KB | Display | FSC data file |
Images | emd_26350.png | 145.5 KB | ||
Filedesc metadata | emd-26350.cif.gz | 5.1 KB | ||
Others | emd_26350_additional_1.map.gz emd_26350_half_map_1.map.gz emd_26350_half_map_2.map.gz | 32.3 MB 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26350 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26350 | HTTPS FTP |
-Validation report
Summary document | emd_26350_validation.pdf.gz | 1.2 MB | Display | EMDB validaton report |
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Full document | emd_26350_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | emd_26350_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | emd_26350_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26350 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26350 | HTTPS FTP |
-Related structure data
Related structure data | 7u5hMC 7u5iC 7u5jC 7u5kC 7u5lC 7u5mC 7u5nC 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_26350.map.gz / Format: CCP4 / Size: 64 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
-Additional map: #1
File | emd_26350_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_26350_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_26350_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dodecamer of Aspartyl Aminopeptidase
Entire | Name: Dodecamer of Aspartyl Aminopeptidase |
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Components |
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-Supramolecule #1: Dodecamer of Aspartyl Aminopeptidase
Supramolecule | Name: Dodecamer of Aspartyl Aminopeptidase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Bos taurus (cattle) |
-Macromolecule #1: Aspartyl aminopeptidase
Macromolecule | Name: Aspartyl aminopeptidase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: aspartyl aminopeptidase |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 51.893188 KDa |
Sequence | String: MSGRARKEAV QAAARELLKF VNRSPSPFHA VAECRSRLLQ AGFHELKETE SWDIKPESKY FLTRNSSTII AFAVGGQYVP GNGFSLIGA HTDSPCLRVK RRSRRSQVGF QQVGVETYGG GIWSTWFDRD LTLAGRVIVK CPTSGRLEQR LVHVDRPILR I PHLAIHLQ ...String: MSGRARKEAV QAAARELLKF VNRSPSPFHA VAECRSRLLQ AGFHELKETE SWDIKPESKY FLTRNSSTII AFAVGGQYVP GNGFSLIGA HTDSPCLRVK RRSRRSQVGF QQVGVETYGG GIWSTWFDRD LTLAGRVIVK CPTSGRLEQR LVHVDRPILR I PHLAIHLQ RNVNENFGPN MEMHLVPILA TSIQEELEKG TPEPGPLNAT DERHHSVLTS LLCAHLGLSP EDILEMELCL AD TQPAVLG GAYEEFIFAP RLDNLHSCFC ALQALIDSCS APASLAADPH VRMIALYDNE EVGSESAQGA QSLLTELVLR RIS ASPQHL TAFEEAIPKS YMISADMAHA VHPNYLDKHE ENHRPLFHKG PVIKVNSKQR YASNAVSEAL IREVASSVGV PLQD LMVRN DSPCGTTIGP ILASRLGLRV LDLGSPQLAM HSIRETACTT GVLQTITLFK GFFELFPSLS RSLLVD UniProtKB: Aspartyl aminopeptidase |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 24 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 (6k x 4k) / Average electron dose: 37.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |