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- EMDB-41452: Cryo-EM structure of monomeric alpha-Klotho -

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Basic information

Entry
Database: EMDB / ID: EMD-41452
TitleCryo-EM structure of monomeric alpha-Klotho
Map datafull map
Sample
  • Complex: Human aKlotho
    • Protein or peptide: Klotho
KeywordsSIGNALING PROTEIN
Function / homology
Function and homology information


norepinephrine biosynthetic process / beta-glucuronidase / FGFR1c and Klotho ligand binding and activation / beta-glucuronidase activity / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / fibroblast growth factor receptor binding / vitamin D binding / energy reserve metabolic process / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 ...norepinephrine biosynthetic process / beta-glucuronidase / FGFR1c and Klotho ligand binding and activation / beta-glucuronidase activity / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / fibroblast growth factor receptor binding / vitamin D binding / energy reserve metabolic process / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / 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 / response to activity / determination of adult lifespan / 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
Glycosyl hydrolases family 1, N-terminal conserved site / Glycosyl hydrolases family 1 N-terminal signature. / Glycosyl hydrolase family 1 / Glycoside hydrolase family 1 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsSchnicker NJ / Xu Z / Mohammad A / Gakhar L / Huang CL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)RO1 DK100605 United States
CitationJournal: To Be Published
Title: Exploring the a-Klotho conformational landscape
Authors: Schnicker NJ / Xu Z / Mohammad A / Gakhar L / Huang CL
History
DepositionAug 3, 2023-
Header (metadata) releaseAug 14, 2024-
Map releaseAug 14, 2024-
UpdateAug 14, 2024-
Current statusAug 14, 2024Processing site: RCSB / Status: Released

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Structure visualization

Downloads & links

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Map

FileDownload / File: emd_41452.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfull map
Voxel sizeX=Y=Z: 0.6507 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.0016833987 - 2.5598834
Average (Standard dev.)0.0017162851 (±0.031842988)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 221.23799 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Human aKlotho

EntireName: Human aKlotho
Components
  • Complex: Human aKlotho
    • Protein or peptide: Klotho

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Supramolecule #1: Human aKlotho

SupramoleculeName: Human aKlotho / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 130 KDa

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Macromolecule #1: Klotho

MacromoleculeName: Klotho / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 109.993688 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.5 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
25.0 mMHEPES
300.0 mMNaCl
1.0 mMTCEP

Details: 25mM HEPES pH7.5, 300mM NaCl, 1mM TCEP
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7891498
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5w21

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115398
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.1)

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Atomic model buiding 1

Initial modelPDB ID:

5w21


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8toh:
Cryo-EM structure of monomeric alpha-Klotho

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