8XI9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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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

  • DOI: https://doi.org/10.1002/1873-3468.14986
  • Primary Citation of 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.


  • Organizational Affiliation

    Graduate School of Science and Engineering, University of Toyama, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FRB-FKBP fusion protein202Homo sapiensMutation(s): 0 
Gene Names: MTORFRAPFRAP1FRAP2RAFT1RAPT1FKBP1AFKBP1FKBP12
EC: 2.7.11.1 (PDB Primary Data), 5.2.1.8 (PDB Primary Data)
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP42345P62942
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RAP (Subject of Investigation/LOI)
Query on RAP

Download Ideal Coordinates CCD File 
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 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.517α = 90
b = 80.517β = 90
c = 122.419γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP18H04544
Japan Society for the Promotion of Science (JSPS)JapanJP19K06595

Revision History  (Full details and data files)

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