8XI9 | pdb_00008xi9

Crystal structure of FRB-FKBP fusion protein in complex with rapamycin

• PDB DOI: https://doi.org/10.2210/pdb8XI9/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-19 Released: 2024-08-07 
• Deposition Author(s): Inobe, T., Sakaguchi, R., Obita, T., Mukaiyama, A., Yokoyama, T., Mizuguchi, M., Akiyama, S.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structural insights into rapamycin-induced oligomerization of a FRB-FKBP fusion protein.

Inobe, T., Sakaguchi, R., Obita, T., Mukaiyama, A., Koike, S., Yokoyama, T., Mizuguchi, M., Akiyama, S.

(2024) FEBS Lett 598: 2292-2305

• PubMed: 39031920 
• DOI: https://doi.org/10.1002/1873-3468.14986
• Primary Citation Related Structures: 
  8XI9


• PubMed Abstract: 
  

  Inducible dimerization systems, such as rapamycin-induced dimerization of FK506 binding protein (FKBP) and FKBP-rapamycin binding (FRB) domain, are widely employed chemical biology tools to manipulate cellular functions. We previously advanced an inducible dimerization system into an inducible oligomerization system by developing a bivalent fusion protein, FRB-FKBP, which forms large oligomers upon rapamycin addition and can be used to manipulate cells. However, the oligomeric structure of FRB-FKBP remains unclear. Here, we report that FRB-FKBP forms a rotationally symmetric trimer in crystals, but a larger oligomer in solution, primarily tetramers and pentamers, which maintain similar inter-subunit contacts as in the crystal trimer. These findings expand the applications of the FRB-FKBP oligomerization system in diverse biological events.

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Organizational Affiliation: 
• Graduate School of Science and Engineering, University of Toyama, Japan.
Faculty of Pharmaceutical Sciences, University of Toyama, Japan.
Research Center of Integrative Molecular Systems (CIMoS), Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Japan.
Molecular Science Program, Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: SAXS

Macromolecule Content 

• Total Structure Weight: 24.24 kDa 
• Atom Count: 1,809 
• Modeled Residue Count: 201 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FRB-FKBP fusion protein	A	202	Homo sapiens	Mutation(s): 0  Gene Names: MTOR, FRAP, FRAP1, FRAP2, RAFT1, RAPT1, FKBP1A, FKBP1, FKBP12 EC: 2.7.11.1 (PDB Primary Data), 5.2.1.8 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens) Explore P42345  Go to UniProtKB:  P42345
PHAROS:  P42345 GTEx:  ENSG00000198793
Find proteins for P62942 (Homo sapiens) Explore P62942  Go to UniProtKB:  P62942
PHAROS:  P62942 GTEx:  ENSG00000088832
UniProt Groups	P42345P62942

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAP (Subject of Investigation/LOI)	B [auth A]	RAPAMYCIN IMMUNOSUPPRESSANT DRUG C51 H79 N O13 QFJCIRLUMZQUOT-HPLJOQBZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.187 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.517	α = 90
b = 80.517	β = 90
c = 122.419	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Inobe, T., Sakaguchi, R., Obita, T., Mukaiyama, A., Yokoyama, T., Mizuguchi, M., Akiyama, S.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	JP18H04544
Japan Society for the Promotion of Science (JSPS)	Japan	JP19K06595

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release
  
• Version 1.1: 2024-10-09
  Changes: Database references, Structure summary