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Yorodumi- PDB-8d44: Cryo-electron microscopy structure of human kidney Fructose-bisph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8d44 | ||||||
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Title | Cryo-electron microscopy structure of human kidney Fructose-bisphosphate aldolase B | ||||||
Components | Fructose-bisphosphate aldolase B | ||||||
Keywords | HYDROLASE / 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 / Fructose catabolism / NADH oxidation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / Gluconeogenesis ...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 / Fructose catabolism / NADH oxidation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / Gluconeogenesis / positive regulation of ATP-dependent activity / fructose metabolic process / negative regulation of pentose-phosphate shunt / fructose 1,6-bisphosphate metabolic process / 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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||
Authors | Lyu, M. / Yu, E.W. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8d44.cif.gz | 256 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8d44.ent.gz | 209.6 KB | Display | PDB format |
PDBx/mmJSON format | 8d44.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8d44_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 8d44_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8d44_validation.xml.gz | 49.7 KB | Display | |
Data in CIF | 8d44_validation.cif.gz | 76.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/8d44 ftp://data.pdbj.org/pub/pdb/validation_reports/d4/8d44 | HTTPS FTP |
-Related structure data
Related structure data | 27174MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Homo sapiens (human) / Gene: ALDOB, ALDB / Production host: Homo sapiens (human) / References: UniProt: P05062, fructose-bisphosphate aldolase |
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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 |
-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: Homo sapiens (human) |
Source (recombinant) | Organism: Homo sapiens (human) |
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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
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) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
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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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