6M4W

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 

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Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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 Pharmacology, Johns Hopkins University School of Medicine, Baltimore, MD, USA. jctinoue@jhmi.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
chimera of Maltose/maltodextrin-binding periplasmic protein and Peptidyl-prolyl cis-trans isomerase FKBP1AA, B, C405Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 5 
Gene Names: malEb4034JW3994FKBP1AFKBP1FKBP12
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
Find proteins for P62942 (Homo sapiens)
Explore P62942 
Go to UniProtKB:  P62942
PHAROS:  P62942
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9P62942
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase FKBP1AD, E, F76Homo 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
Entity Groups  
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UniProt GroupP62942
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase mTORG, H, I95Homo sapiensMutation(s): 1 
Gene Names: MTORFRAPFRAP1FRAP2RAFT1RAPT1
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
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UniProt GroupP42345
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranoseJ, K, L 2N/A Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RAP (Subject of Investigation/LOI)
Query on RAP

Download Ideal Coordinates CCD File 
M [auth D],
N [auth E],
O [auth F]
RAPAMYCIN IMMUNOSUPPRESSANT DRUG
C51 H79 N O13
QFJCIRLUMZQUOT-HPLJOQBZSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
P [auth G]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
J, K, Lalpha-maltoseOligosaccharide / Nutrient Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.11 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.238 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.546α = 90
b = 127.546β = 90
c = 278.557γ = 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 1.1: 2020-09-16
    Changes: Database references