6M4U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41592-020-0913-x
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1AA,
C [auth E]
110Homo sapiensMutation(s): 0 
Gene Names: FKBP1AFKBP1FKBP12
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 Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62942
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTORB,
D [auth F]
95Homo sapiensMutation(s): 1 
Gene Names: MTOR
EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens)
Explore P42345 
Go to UniProtKB:  P42345
PHAROS:  P42345
GTEx:  ENSG00000198793 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42345
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RAP (Subject of Investigation/LOI)
Query on RAP

Download Ideal Coordinates CCD File 
E [auth A],
R [auth E]
RAPAMYCIN IMMUNOSUPPRESSANT DRUG
C51 H79 N O13
QFJCIRLUMZQUOT-HPLJOQBZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
X [auth F]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth F]
F [auth A]
G [auth A]
H [auth A]
K [auth B]
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
Query on CL

Download Ideal Coordinates CCD File 
BA [auth F]
I [auth A]
J [auth A]
P [auth B]
Q [auth B]
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
Binding Affinity Annotations 
IDSourceBinding Affinity
RAP BindingDB:  6M4U Ki: min: 0.2, max: 1 (nM) from 2 assay(s)
Kd: min: 0.3, max: 0.6 (nM) from 2 assay(s)
IC50: min: 0.05, max: 430 (nM) from 10 assay(s)
EC50: min: 30, max: 36 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.034α = 90
b = 67.419β = 107.2
c = 69.793γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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