+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41452 | |||||||||
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Title | Cryo-EM structure of monomeric alpha-Klotho | |||||||||
Map data | full map | |||||||||
Sample |
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Keywords | SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information norepinephrine biosynthetic process / beta-glucuronidase / FGFR1c and Klotho ligand binding and activation / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / beta-glucuronidase activity / fibroblast growth factor receptor binding / vitamin D binding / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / energy reserve metabolic process ...norepinephrine biosynthetic process / beta-glucuronidase / FGFR1c and Klotho ligand binding and activation / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / beta-glucuronidase activity / fibroblast growth factor receptor binding / vitamin D binding / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / energy reserve metabolic process / response to vitamin D / negative regulation of systemic arterial blood pressure / response to angiotensin / beta-glucosidase activity / fibroblast growth factor binding / PI-3K cascade:FGFR1 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / positive regulation of bone mineralization / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / determination of adult lifespan / response to activity / Negative regulation of FGFR1 signaling / hormone activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / carbohydrate metabolic process / apical plasma membrane / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.29 Å | |||||||||
Authors | Schnicker NJ / Xu Z / Mohammad A / Gakhar L / Huang CL | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Exploring the a-Klotho conformational landscape Authors: Schnicker NJ / Xu Z / Mohammad A / Gakhar L / Huang CL | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41452.map.gz | 132.9 MB | EMDB map data format | |
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Header (meta data) | emd-41452-v30.xml emd-41452.xml | 16.9 KB 16.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41452_fsc.xml | 11.3 KB | Display | FSC data file |
Images | emd_41452.png | 91.3 KB | ||
Filedesc metadata | emd-41452.cif.gz | 6.3 KB | ||
Others | emd_41452_half_map_1.map.gz emd_41452_half_map_2.map.gz | 139.2 MB 139.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41452 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41452 | HTTPS FTP |
-Validation report
Summary document | emd_41452_validation.pdf.gz | 723.6 KB | Display | EMDB validaton report |
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Full document | emd_41452_full_validation.pdf.gz | 723.1 KB | Display | |
Data in XML | emd_41452_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | emd_41452_validation.cif.gz | 25.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41452 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41452 | HTTPS FTP |
-Related structure data
Related structure data | 8tohMC 8uf8C 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_41452.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | full map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.6507 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map B
File | emd_41452_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_41452_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human aKlotho
Entire | Name: Human aKlotho |
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Components |
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-Supramolecule #1: Human aKlotho
Supramolecule | Name: Human aKlotho / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 130 KDa |
-Macromolecule #1: Klotho
Macromolecule | Name: Klotho / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 109.993688 KDa |
Recombinant expression | Organism: Mus musculus (house mouse) |
Sequence | String: EPGDGAQTWA RFSRPPAPEA AGLFQGTFPD GFLWAVGSAA YQTEGGWQQH GKGASIWDTF THHPLAPPGD SRNASLPLGA PSPLQPATG DVASDSYNNV FRDTEALREL GVTHYRFSIS WARVLPNGSA GVPNREGLRY YRRLLERLRE LGVQPVVTLY H WDLPQRLQ ...String: EPGDGAQTWA RFSRPPAPEA AGLFQGTFPD GFLWAVGSAA YQTEGGWQQH GKGASIWDTF THHPLAPPGD SRNASLPLGA PSPLQPATG DVASDSYNNV FRDTEALREL GVTHYRFSIS WARVLPNGSA GVPNREGLRY YRRLLERLRE LGVQPVVTLY H WDLPQRLQ DAYGGWANRA LADHFRDYAE LCFRHFGGQV KYWITIDNPY VVAWHGYATG RLAPGIRGSP RLGYLVAHNL LL AHAKVWH LYNTSFRPTQ GGQVSIALSS HWINPRRMTD HSIKECQKSL DFVLGWFAKP VFIDGDYPES MKNNLSSILP DFT ESEKKF IKGTADFFAL CFGPTLSFQL LDPHMKFRQL ESPNLRQLLS WIDLEFNHPQ IFIVENGWFV SGTTKRDDAK YMYY LKKFI METLKAIKLD GVDVIGYTAW SLMDGFEWHR GYSIRRGLFY VDFLSQDKML LPKSSALFYQ KLIEKNGFPP LPENQ PLEG TFPCDFAWGV VDNYIQVDTT LSQFTDLNVY LWDVHHSKRL IKVDGVVTKK RKSYCVDFAA IQPQIALLQE MHVTHF RFS LDWALILPLG NQSQVNHTIL QYYRCMASEL VRVNITPVVA LWQPMAPNQG LPRLLARQGA WENPYTALAF AEYARLC FQ ELGHHVKLWI TMNEPYTRNM TYSAGHNLLK AHALAWHVYN EKFRHAQNGK ISIALQADWI EPACPFSQKD KEVAERVL E FDIGWLAEPI FGSGDYPWVM RDWLNQRNNF LLPYFTEDEK KLIQGTFDFL ALSHYTTILV DSEKEDPIKY NDYLEVQEM TDITWLNSPS QVAVVPWGLR KVLNWLKFKY GDLPMYIISN GIDDGLHAED DQLRVYYMQN YINEALKAHI LDGINLCGYF AYSFNDRTA PRFGLYRYAA DQFEPKASMK HYRKIIDSNG FPGPETLERF CPEEFTVCTE CSFFHTRKSH HHHHH UniProtKB: Klotho |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL | ||||||||
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Buffer | pH: 7.5 Component:
Details: 25mM HEPES pH7.5, 300mM NaCl, 1mM TCEP | ||||||||
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR | ||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8676 / Average exposure time: 1.099 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |