6M4U | pdb_00006m4u

Crystal structure of FKBP-FRB T2098L mutant in complex with rapamycin

• PDB DOI: https://doi.org/10.2210/pdb6M4U/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2020-03-09 Released: 2020-08-26 
• Deposition Author(s): Kikuchi, M., Wu, D., Inoue, T., Umehara, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.258 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

Literature

Rational design and implementation of a chemically inducible heterotrimerization system.

Wu, H.D., Kikuchi, M., Dagliyan, O., Aragaki, A.K., Nakamura, H., Dokholyan, N.V., Umehara, T., Inoue, T.

(2020) Nat Methods 17: 928-936

• PubMed: 32747768 
• DOI: https://doi.org/10.1038/s41592-020-0913-x
• Primary Citation Related Structures: 
  6M4U, 6M4V, 6M4W


• PubMed Abstract: 
  

  Chemically inducible dimerization (CID) uses a small molecule to induce binding of two different proteins. CID tools such as the FK506-binding protein-FKBP-rapamycin-binding- (FKBP-FRB)-rapamycin system have been widely used to probe molecular events inside and outside cells. While various CID tools are available, chemically inducible trimerization (CIT) does not exist, due to inherent challenges in designing a chemical that simultaneously binds three proteins with high affinity and specificity. Here, we developed CIT by rationally splitting FRB and FKBP. Cellular and structural datasets showed efficient trimerization of split pairs of FRB or FKBP with full-length FKBP or FRB, respectively, by rapamycin. CIT rapidly induced tri-organellar junctions and perturbed intended membrane lipids exclusively at select membrane contact sites. By conferring one additional condition to what is achievable with CID, CIT expands the types of manipulation in single live cells to address cell biology questions otherwise intractable and engineer cell functions for future synthetic biology applications.

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Organizational Affiliation: 
• Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan.
Department of Neurobiology, Harvard Medical School, Boston, MA, USA.
Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Kyoto University Graduate School of Engineering, Department of Synthetic Chemistry and Biological Chemistry, Katsura Int'tech Center, Graduate School of Engineering, Kyoto University, Nishikyo-ku, Kyoto, Japan.
Departments of Pharmacology and Biochemistry & Molecular Biology, Penn State University College of Medicine, Hershey, PA, USA.
Departments of Chemistry and Biomedical Engineering, Pennsylvania State University, University Park, PA, USA.
Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Kanagawa, Japan. [e-mail].
Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA. [e-mail].
Department of Cell Biology, Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD, USA. [e-mail].
Department of Pharmacology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.2 kDa 
• Atom Count: 3,724 
• Modeled Residue Count: 406 
• Deposited Residue Count: 410 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase FKBP1A	A, C [auth E]	110	Homo sapiens	Mutation(s): 0  Gene Names: FKBP1A, FKBP1, FKBP12 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62942 (Homo sapiens) Explore P62942  Go to UniProtKB:  P62942
PHAROS:  P62942 GTEx:  ENSG00000088832

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein kinase mTOR	B, D [auth F]	95	Homo sapiens	Mutation(s): 1  Gene Names: MTOR EC: 2.7.11.1 (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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAP (Subject of Investigation/LOI)	E [auth A], R [auth E]	RAPAMYCIN IMMUNOSUPPRESSANT DRUG C51 H79 N O13 QFJCIRLUMZQUOT-HPLJOQBZSA-N
GOL	X [auth F]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	AA [auth F], F [auth A], G [auth A], H [auth A], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B], S [auth E], V [auth F], W [auth F], Y [auth F], Z [auth F]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	BA [auth F], I [auth A], J [auth A], P [auth B], Q [auth B], T [auth E], U [auth E]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.258 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.034	α = 90
b = 67.419	β = 107.2
c = 69.793	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
MOLREP	phasing
REFMAC	refinement
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-08-26 
Deposition Author(s): Kikuchi, M., Wu, D., Inoue, T., Umehara, T.

Revision History  

• Version 1.0: 2020-08-26
  Type: Initial release
  
• Version 2.0: 2020-09-02
  Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2020-09-16
  Changes: Database references
• Version 2.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description