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- EMDB-26352: Cryo-EM Structure of ALDOA -

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Basic information

Entry
Database: EMDB / ID: EMD-26352
TitleCryo-EM Structure of ALDOA
Map data
Sample
  • Complex: Tetramer of aldolase
    • Protein or peptide: Fructose-bisphosphate aldolase
  • Ligand: water
Function / homologyFructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / Aldolase-type TIM barrel / Fructose-bisphosphate aldolase
Function and homology information
Biological speciesBos taurus (cattle) / cattle (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 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_26352.png

Downloads & links

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Map

FileDownload / File: emd_26352.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-2.9236152 - 3.6168628
Average (Standard dev.)1.9770008e-05 (±0.06920883)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
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_26352_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_26352_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_26352_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 aldolase

EntireName: Tetramer of aldolase
Components
  • Complex: Tetramer of aldolase
    • Protein or peptide: Fructose-bisphosphate aldolase
  • Ligand: water

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Supramolecule #1: Tetramer of aldolase

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

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Macromolecule #1: Fructose-bisphosphate aldolase

MacromoleculeName: Fructose-bisphosphate aldolase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: fructose-bisphosphate aldolase
Source (natural)Organism: cattle (cattle)
Molecular weightTheoretical: 39.488105 KDa
SequenceString: MPHQYPALTP EQKKELCDIA HRIVAPGKGI LAADESTGSI AKRLQSIGTE NTEENRRFYR QLLLTADDRV NPCIGGVILF HETLYQKAD DGRPFPQVIK AKGGVVGIKV DKGVVPLAGT NGETTTQGLD GLSERCAQYK KDGADFAKWR CVLKIGEHTP S SLAIMENA ...String:
MPHQYPALTP EQKKELCDIA HRIVAPGKGI LAADESTGSI AKRLQSIGTE NTEENRRFYR QLLLTADDRV NPCIGGVILF HETLYQKAD DGRPFPQVIK AKGGVVGIKV DKGVVPLAGT NGETTTQGLD GLSERCAQYK KDGADFAKWR CVLKIGEHTP S SLAIMENA NVLARYASIC QQNGIVPIVE PEILPDGDHD LKRCQYVTEK VLAAVYKALS DHHIYLEGTL LKPNMVTPGH AC TQKYSHE EIAMATVTAL RRTVPPAVPG ITFLSGGQSE EEASINLNAI NKCPLLKPWA LTFSYGRALQ ASALKAWGGK KEN LKAAQE EYVKRALANS LACQGKYTPS GKAGAAASES LFISNHAY

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 284 / 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: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3) / Number images used: 14361
FSC plot (resolution estimation)

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