+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26355 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM Structure of GAPDH | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | GAPDH / glyceraldehyde-3-phosphate dehydrogenase / TRANSFERASE | |||||||||
Function / homology | Function and homology information regulation of neurotransmitter loading into synaptic vesicle / Glycolysis / Gluconeogenesis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / extrinsic component of synaptic vesicle membrane / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / GAIT complex ...regulation of neurotransmitter loading into synaptic vesicle / Glycolysis / Gluconeogenesis / peptidyl-cysteine S-trans-nitrosylation / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / extrinsic component of synaptic vesicle membrane / glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity / GAIT complex / positive regulation of type I interferon production / glycolytic process / microtubule cytoskeleton organization / glucose metabolic process / NAD binding / microtubule cytoskeleton / disordered domain specific binding / regulation of translation / NADP binding / microtubule binding / neuron apoptotic process / positive regulation of canonical NF-kappaB signal transduction / protein stabilization / innate immune response / nucleus / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.28 Å | |||||||||
Authors | Morgan CE / Zhang Z / Yu EW | |||||||||
Funding support | United States, 1 items
| |||||||||
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 |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_26355.map.gz | 3.8 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-26355-v30.xml emd-26355.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_26355_fsc.xml | 8.3 KB | Display | FSC data file |
Images | emd_26355.png | 108.9 KB | ||
Filedesc metadata | emd-26355.cif.gz | 5 KB | ||
Others | emd_26355_additional_1.map.gz emd_26355_half_map_1.map.gz emd_26355_half_map_2.map.gz | 32.4 MB 59.1 MB 59.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26355 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26355 | HTTPS FTP |
-Validation report
Summary document | emd_26355_validation.pdf.gz | 672.3 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_26355_full_validation.pdf.gz | 671.9 KB | Display | |
Data in XML | emd_26355_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_26355_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26355 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26355 | HTTPS FTP |
-Related structure data
Related structure data | 7u5mMC 7u5hC 7u5iC 7u5jC 7u5kC 7u5lC 7u5nC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_26355.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Additional map: #1
File | emd_26355_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_26355_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_26355_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Tetramer of GAPDH
Entire | Name: Tetramer of GAPDH |
---|---|
Components |
|
-Supramolecule #1: Tetramer of GAPDH
Supramolecule | Name: Tetramer of GAPDH / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
---|---|
Source (natural) | Organism: Bos taurus (cattle) |
-Macromolecule #1: Glyceraldehyde-3-phosphate dehydrogenase
Macromolecule | Name: Glyceraldehyde-3-phosphate dehydrogenase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO EC number: glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) |
---|---|
Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 35.914043 KDa |
Sequence | String: MVKVGVNGFG RIGRLVTRAA FNSGKVDIVA INDPFIDLHY MVYMFQYDST HGKFNGTVKA ENGKLVINGK AITIFQERDP ANIKWGDAG AEYVVESTGV FTTMEKAGAH LKGGAKRVII SAPSADAPMF VMGVNHEKYN NTLKIVSNAS CTTNCLAPLA K VIHDHFGI ...String: MVKVGVNGFG RIGRLVTRAA FNSGKVDIVA INDPFIDLHY MVYMFQYDST HGKFNGTVKA ENGKLVINGK AITIFQERDP ANIKWGDAG AEYVVESTGV FTTMEKAGAH LKGGAKRVII SAPSADAPMF VMGVNHEKYN NTLKIVSNAS CTTNCLAPLA K VIHDHFGI VEGLMTTVHA ITATQKTVDG PSGKLWRDGR GAAQNIIPAS TGAAKAVGKV IPELNGKLTG MAFRVPTPNV SV VDLTCRL EKPAKYDEIK KVVKQASEGP LKGILGYTED QVVSCDFNSD THSSTFDAGA GIALNDHFVK LISWYDNEFG YSN RVVDLM VHMASKE UniProtKB: Glyceraldehyde-3-phosphate dehydrogenase |
-Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Macromolecule | Name: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD |
---|---|
Molecular weight | Theoretical: 663.425 Da |
Chemical component information | ChemComp-NAD: |
-Macromolecule #3: water
Macromolecule | Name: water / type: ligand / ID: 3 / Number of copies: 399 / Formula: HOH |
---|---|
Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 36.0 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 |