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- PDB-8d44: Cryo-electron microscopy structure of human kidney Fructose-bisph... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8d44 | |||||||||||||||||||||||||||||||||||||||
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Title | Cryo-electron microscopy structure of human kidney Fructose-bisphosphate aldolase B | |||||||||||||||||||||||||||||||||||||||
![]() | Fructose-bisphosphate aldolase B | |||||||||||||||||||||||||||||||||||||||
![]() | HYDROLASE / fructose-bisphosphate aldolase B / ALDOB | |||||||||||||||||||||||||||||||||||||||
Function / homology | ![]() 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 / gluconeogenesis / glycolytic process / centriolar satellite / ATPase binding / molecular adaptor activity / extracellular exosome / identical protein binding / cytosol Similarity search - Function | |||||||||||||||||||||||||||||||||||||||
Biological species | ![]() | |||||||||||||||||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||||||||||||||||||||||||||||||||
![]() | Lyu, M. / Yu, E.W. | |||||||||||||||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-electron microscopy structure of human kidney Fructose-bisphosphate aldolase B Authors: Lyu, M. / Yu, E.W. | |||||||||||||||||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 256.5 KB | Display | ![]() |
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PDB format | ![]() | 209.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 49.8 KB | Display | |
Data in CIF | ![]() | 76.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 27174MC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 39519.969 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Has protein modification | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Fructose-bisphosphate aldolase B / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: 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 |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm |
Image recording | Electron dose: 39 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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EM software | Name: PHENIX / Category: model refinement | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126024 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL | ||||||||||||||||||||||||
Refine LS restraints |
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