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- EMDB-27174: Cryo-electron microscopy structure of human kidney Fructose-bisph... -

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Basic information

Entry
Database: EMDB / ID: EMD-27174
TitleCryo-electron microscopy structure of human kidney Fructose-bisphosphate aldolase B
Map data
Sample
  • Complex: Fructose-bisphosphate aldolase B
    • Protein or peptide: Fructose-bisphosphate aldolase B
Keywordsfructose-bisphosphate aldolase B / ALDOB / HYDROLASE
Function / homology
Function and homology information


Hereditary fructose intolerance / fructose-1-phosphate aldolase activity / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / vacuolar proton-transporting V-type ATPase complex assembly / fructose binding / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis ...Hereditary fructose intolerance / fructose-1-phosphate aldolase activity / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / vacuolar proton-transporting V-type ATPase complex assembly / fructose binding / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / Gluconeogenesis / fructose metabolic process / negative regulation of pentose-phosphate shunt / Glycolysis / microtubule organizing center / cytoskeletal protein binding / glycolytic process / gluconeogenesis / centriolar satellite / ATPase binding / molecular adaptor activity / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase-type TIM barrel
Similarity search - Domain/homology
Fructose-bisphosphate aldolase B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLyu M / Yu EW
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI145069 United States
CitationJournal: To Be Published
Title: Cryo-electron microscopy structure of human kidney Fructose-bisphosphate aldolase B
Authors: Lyu M / Yu EW
History
DepositionJun 1, 2022-
Header (metadata) releaseNov 16, 2022-
Map releaseNov 16, 2022-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27174.png

Downloads & links

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Map

FileDownload / File: emd_27174.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å		1.07 Å/pix.
x 300 pix.
= 321. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-2.1647909 - 3.2147505
Average (Standard dev.)-0.0000033704448 (±0.055016197)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 321.00003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_27174_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_27174_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 : Fructose-bisphosphate aldolase B

EntireName: Fructose-bisphosphate aldolase B
Components
  • Complex: Fructose-bisphosphate aldolase B
    • Protein or peptide: Fructose-bisphosphate aldolase B

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Supramolecule #1: Fructose-bisphosphate aldolase B

SupramoleculeName: Fructose-bisphosphate aldolase B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fructose-bisphosphate aldolase B

MacromoleculeName: Fructose-bisphosphate aldolase B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: fructose-bisphosphate aldolase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.519969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAHRFPALTQ EQKKELSEIA QSIVANGKGI LAADESVGTM GNRLQRIKVE NTEENRRQFR EILFSVDSSI NQSIGGVILF HETLYQKDS QGKLFRNILK EKGIVVGIKL DQGGAPLAGT NKETTIQGLD GLSERCAQYK KDGVDFGKWR AVLRIADQCP S SLAIQENA ...String:
MAHRFPALTQ EQKKELSEIA QSIVANGKGI LAADESVGTM GNRLQRIKVE NTEENRRQFR EILFSVDSSI NQSIGGVILF HETLYQKDS QGKLFRNILK EKGIVVGIKL DQGGAPLAGT NKETTIQGLD GLSERCAQYK KDGVDFGKWR AVLRIADQCP S SLAIQENA NALARYASIC QQNGLVPIVE PEVIPDGDHD LEHCQYVTEK VLAAVYKALN DHHVYLEGTL LKPNMVTAGH AC TKKYTPE QVAMATVTAL HRTVPAAVPG ICFLSGGMSE EDATLNLNAI NLCPLPKPWK LSFSYGRALQ ASALAAWGGK AAN KEATQE AFMKRAMANC QAAKGQYVHT GSSGAASTQS LFTACYTY

UniProtKB: Fructose-bisphosphate aldolase B

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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

Concentration.7 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK I / Details: blot 15 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 126024
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: OTHER
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-8d44:
Cryo-electron microscopy structure of human kidney Fructose-bisphosphate aldolase B

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