8TOH | pdb_00008toh

Cryo-EM structure of monomeric alpha-Klotho

• PDB DOI: https://doi.org/10.2210/pdb8TOH/pdb
• EM Map EMD-41452: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2023-08-03 Released: 2024-08-14 
• Deposition Author(s): Schnicker, N.J., Xu, Z., Mohammad, A., Gakhar, L., Huang, C.L.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Conformational landscape of soluble alpha-klotho revealed by cryogenic electron microscopy.

Schnicker, N.J., Xu, Z., Amir, M., Gakhar, L., Huang, C.L.

(2025) Sci Rep 15: 543-543

• PubMed: 39747283 
• DOI: https://doi.org/10.1038/s41598-024-84246-x
• Primary Citation Related Structures: 
  8TOH, 8UF8


• PubMed Abstract: 
  

  α-Klotho (KLA) is a type-1 membranous protein that can associate with fibroblast growth factor receptor (FGFR) to form co-receptor for FGF23. The ectodomain of unassociated KLA is shed as soluble KLA (sKLA) to exert FGFR/FGF23-independent pleiotropic functions. The previously determined X-ray crystal structure of the extracellular region of sKLA in complex with FGF23 and FGFR1c suggests that sKLA functions solely as an on-demand coreceptor for FGF23. To understand the FGFR/FGF23-independent pleiotropic functions of sKLA, we investigated biophysical properties and structure of apo-sKLA. Single particle cryogenic electron microscopy (cryo-EM) revealed a 3.3 Å resolution structure of apo-sKLA that overlays well with its counterpart in the ternary complex with several distinct features. Compared to the ternary complex, the KL2 domain of apo-sKLA is more flexible. Three-dimensional variability analysis revealed that apo-sKLA adopts conformations with different KL1-KL2 interdomain bending and rotational angles. Mass photometry revealed that sKLA can form a stable structure with FGFR and/or FGF23 as well as sKLA dimer in solution. Cryo-EM supported the dimeric structure of sKLA. Recent studies revealed that FGF23 contains two KLA-binding sites. Our computational studies revealed that each site binds separate KLA in the dimer. The potential multiple forms and shapes of sKLA support its role as FGFR-independent hormone with pleiotropic functions. The ability of FGF23 to engage two KLA's simultaneously raises a potential new mechanism of action for FGF23-mediated signaling by the membranous klotho.

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Organizational Affiliation: 
• Protein and Crystallography Facility, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA. [e-mail].
Department of Molecular Physiology and Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA. [e-mail].
Protein and Crystallography Facility, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.
Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA.
Department of Biochemistry and Molecular Biology, University of Iowa, Iowa City, IA, 52242, USA.
Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 109.99 kDa 
• Atom Count: 7,022 
• Modeled Residue Count: 860 
• Deposited Residue Count: 954 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Klotho	A	954	Homo sapiens	Mutation(s): 0  Gene Names: KL EC: 3.2.1.31
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UEF7 (Homo sapiens) Explore Q9UEF7  Go to UniProtKB:  Q9UEF7
PHAROS:  Q9UEF7 GTEx:  ENSG00000133116

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-14 
Deposition Author(s): Schnicker, N.J., Xu, Z., Mohammad, A., Gakhar, L., Huang, C.L.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	RO1 DK100605

Revision History  

• Version 1.0: 2024-08-14
  Type: Initial release
  
• Version 1.1: 2025-02-26
  Changes: Data collection, Database references, Structure summary