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- PDB-8d44: Cryo-electron microscopy structure of human kidney Fructose-bisph... -

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Basic information

Entry
Database: PDB / ID: 8d44
TitleCryo-electron microscopy structure of human kidney Fructose-bisphosphate aldolase B
ComponentsFructose-bisphosphate aldolase B
KeywordsHYDROLASE / fructose-bisphosphate aldolase B / ALDOB
Function / homology
Function and homology information


fructose-1-phosphate aldolase activity / Hereditary fructose intolerance / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / fructose binding / vacuolar proton-transporting V-type ATPase complex assembly / NADH oxidation / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process ...fructose-1-phosphate aldolase activity / Hereditary fructose intolerance / fructose catabolic process to hydroxyacetone phosphate and glyceraldehyde-3-phosphate / fructose binding / vacuolar proton-transporting V-type ATPase complex assembly / NADH oxidation / Fructose catabolism / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / fructose metabolic process / Gluconeogenesis / positive regulation of ATP-dependent activity / negative regulation of pentose-phosphate shunt / Glycolysis / microtubule organizing center / centriolar satellite / cytoskeletal protein binding / gluconeogenesis / glycolytic process / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLyu, M. / Yu, E.W.
Funding support United States, 1items
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, E.W.
History
DepositionJun 1, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
D: Fructose-bisphosphate aldolase B
C: Fructose-bisphosphate aldolase B
B: Fructose-bisphosphate aldolase B
A: Fructose-bisphosphate aldolase B


Theoretical massNumber of molelcules
Total (without water)158,0804
Polymers158,0804
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Fructose-bisphosphate aldolase B / Liver-type aldolase


Mass: 39519.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDOB, ALDB / Production host: Homo sapiens (human) / References: UniProt: P05062, fructose-bisphosphate aldolase

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Fructose-bisphosphate aldolase B / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
SpecimenConc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.5 K / Details: blot 15 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 39 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126024 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00410648
ELECTRON MICROSCOPYf_angle_d0.60714396
ELECTRON MICROSCOPYf_dihedral_angle_d4.5031460
ELECTRON MICROSCOPYf_chiral_restr0.0431624
ELECTRON MICROSCOPYf_plane_restr0.0061888

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