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

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Basic information

Entry
Database: PDB / ID: 8toh
TitleCryo-EM structure of monomeric alpha-Klotho
ComponentsKlotho
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsSchnicker, N.J. / Xu, Z. / Mohammad, A. / Gakhar, L. / Huang, C.L.
Funding support United States, 1items
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, N.J. / Xu, Z. / Mohammad, A. / Gakhar, L. / Huang, C.L.
History
DepositionAug 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Klotho


Theoretical massNumber of molelcules
Total (without water)109,9941
Polymers109,9941
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Klotho


Mass: 109993.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KL / Cell line (production host): myeloma / Production host: Mus musculus (house mouse) / References: UniProt: Q9UEF7

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human aKlotho / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.13 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7.5 / Details: 25mM HEPES pH7.5, 300mM NaCl, 1mM TCEP
Buffer component
IDConc.FormulaBuffer-ID
125 mMHEPES1
2300 mMNaCl1
31 mMTCEP1
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 279 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.099 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 8676

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Processing

EM software
IDNameVersionCategory
4cryoSPARC3.3.1CTF correction
7UCSF Chimeramodel fitting
9cryoSPARC3.3.1initial Euler assignment
10cryoSPARC3.3.1final Euler assignment
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7891498
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 115398 / Symmetry type: POINT
Atomic model buildingPDB-ID: 5w21

5w21


Pdb chain-ID: A / Accession code: 5w21 / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027252
ELECTRON MICROSCOPYf_angle_d0.5339868
ELECTRON MICROSCOPYf_dihedral_angle_d4.743949
ELECTRON MICROSCOPYf_chiral_restr0.0411011
ELECTRON MICROSCOPYf_plane_restr0.0041276

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