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- EMDB-26355: Cryo-EM Structure of GAPDH -

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Basic information

Entry
Database: EMDB / ID: EMD-26355
TitleCryo-EM Structure of GAPDH
Map data
Sample
  • Complex: Tetramer of GAPDH
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: water
Function / homology
Function and homology information


regulation of neurotransmitter loading into synaptic vesicle / Glycolysis / Gluconeogenesis / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / 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 / Transferases; Transferring nitrogenous groups; Transferring other nitrogenous groups / peptidyl-cysteine S-nitrosylase activity / peptidyl-cysteine S-trans-nitrosylation / 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 / cytosol / cytoplasm
Similarity search - Function
Glyceraldehyde-3-phosphate dehydrogenase, type I / Glyceraldehyde 3-phosphate dehydrogenase, active site / Glyceraldehyde 3-phosphate dehydrogenase active site. / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD(P) binding domain / Glyceraldehyde 3-phosphate dehydrogenase, catalytic domain / Glyceraldehyde/Erythrose phosphate dehydrogenase family / Glyceraldehyde 3-phosphate dehydrogenase, C-terminal domain / Glyceraldehyde 3-phosphate dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Glyceraldehyde-3-phosphate dehydrogenase
Similarity search - Component
Biological speciesBos taurus (cattle) / cattle (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.28 Å
AuthorsMorgan CE / Zhang Z / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: 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
DepositionMar 2, 2022-
Header (metadata) releaseDec 14, 2022-
Map releaseDec 14, 2022-
UpdateJan 11, 2023-
Current statusJan 11, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26355.png

Downloads & links

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Map

FileDownload / File: emd_26355.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-3.7658417 - 5.893564
Average (Standard dev.)1.5817386e-05 (±0.108464666)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_26355_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26355_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_26355_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetramer of GAPDH

EntireName: Tetramer of GAPDH
Components
  • Complex: Tetramer of GAPDH
    • Protein or peptide: Glyceraldehyde-3-phosphate dehydrogenaseGlyceraldehyde 3-phosphate dehydrogenase
  • Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE
  • Ligand: water

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Supramolecule #1: Tetramer of GAPDH

SupramoleculeName: Tetramer of GAPDH / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: Glyceraldehyde-3-phosphate dehydrogenase

MacromoleculeName: 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: cattle (cattle)
Molecular weightTheoretical: 35.914043 KDa
SequenceString: 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

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Macromolecule #2: NICOTINAMIDE-ADENINE-DINUCLEOTIDE

MacromoleculeName: NICOTINAMIDE-ADENINE-DINUCLEOTIDE / type: ligand / ID: 2 / Number of copies: 4 / Formula: NAD
Molecular weightTheoretical: 663.425 Da
Chemical component information

ChemComp-NAD:
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NAD*YM / Nicotinamide adenine dinucleotide

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 399 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 36.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3) / Number images used: 182450
FSC plot (resolution estimation)

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