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Yorodumi- EMDB-27174: Cryo-electron microscopy structure of human kidney Fructose-bisph... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27174 | |||||||||
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Title | Cryo-electron microscopy structure of human kidney Fructose-bisphosphate aldolase B | |||||||||
Map data | ||||||||||
Sample |
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Keywords | fructose-bisphosphate aldolase B / ALDOB / HYDROLASE | |||||||||
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 | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Lyu M / Yu EW | |||||||||
Funding support | United States, 1 items
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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 EW | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27174.map.gz | 97.2 MB | EMDB map data format | |
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Header (meta data) | emd-27174-v30.xml emd-27174.xml | 13.3 KB 13.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27174_fsc.xml | 13.7 KB | Display | FSC data file |
Images | emd_27174.png | 105.2 KB | ||
Filedesc metadata | emd-27174.cif.gz | 5.1 KB | ||
Others | emd_27174_half_map_1.map.gz emd_27174_half_map_2.map.gz | 95.3 MB 95.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27174 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27174 | HTTPS FTP |
-Validation report
Summary document | emd_27174_validation.pdf.gz | 780.1 KB | Display | EMDB validaton report |
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Full document | emd_27174_full_validation.pdf.gz | 779.6 KB | Display | |
Data in XML | emd_27174_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_27174_validation.cif.gz | 23.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27174 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27174 | HTTPS FTP |
-Related structure data
Related structure data | 8d44MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_27174.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_27174_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_27174_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Fructose-bisphosphate aldolase B
Entire | Name: Fructose-bisphosphate aldolase B |
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Components |
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-Supramolecule #1: Fructose-bisphosphate aldolase B
Supramolecule | Name: Fructose-bisphosphate aldolase B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Fructose-bisphosphate aldolase B
Macromolecule | Name: Fructose-bisphosphate aldolase B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: fructose-bisphosphate aldolase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 39.519969 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | .7 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.5 K / Instrument: FEI VITROBOT MARK I / Details: blot 15 seconds before plunging. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 39.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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Output model | PDB-8d44: |