6SGE

Crystal structure of Human RHOB-GTP in complex with nanobody B6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 

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This is version 1.1 of the entry. See complete history


Literature

A Targeted Protein Degradation Cell-Based Screening for Nanobodies Selective toward the Cellular RHOB GTP-Bound Conformation.

Bery, N.Keller, L.Soulie, M.Gence, R.Iscache, A.L.Cherier, J.Cabantous, S.Sordet, O.Lajoie-Mazenc, I.Pedelacq, J.D.Favre, G.Olichon, A.

(2019) Cell Chem Biol 26: 1544

  • DOI: https://doi.org/10.1016/j.chembiol.2019.08.009
  • Primary Citation of Related Structures:  
    6HXU, 6SGE

  • PubMed Abstract: 
  • The selective downregulation of activated intracellular proteins is a key challenge in cell biology. RHO small GTPases switch between a guanosine diphosphate (GDP)-bound and a guanosine triphosphate (GTP)-bound state that drives downstream signaling. At present, no tool is available to study endogenous RHO-GTPinduced conformational changes in live cells ...

    The selective downregulation of activated intracellular proteins is a key challenge in cell biology. RHO small GTPases switch between a guanosine diphosphate (GDP)-bound and a guanosine triphosphate (GTP)-bound state that drives downstream signaling. At present, no tool is available to study endogenous RHO-GTPinduced conformational changes in live cells. Here, we established a cell-based screen to selectively degrade RHOB-GTP using F-box-intracellular single-domain antibody fusion. We identified one intracellular antibody (intrabody) that shows selective targeting of endogenous RHOB-GTP mediated by interactions between the CDR3 loop of the domain antibody and the GTP-binding pocket of RHOB. Our results suggest that, while RHOB is highly regulated at the expression level, only the GTP-bound pool, but not its global expression, mediates RHOB functions in genomic instability and in cell invasion. The F-box/intrabody-targeted protein degradation represents a unique approach to knock down the active form of small GTPases or other proteins with multiple cellular activities.


    Organizational Affiliation

    Centre de Recherche en Cancérologie de Toulouse (CRCT), INSERM, Université de Toulouse, CNRS, UPS, Toulouse, France. Electronic address: aurelien.olichon@inserm.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rho-related GTP-binding protein RhoB
A, C
183Homo sapiensMutation(s): 1 
Gene Names: RHOBARH6ARHB
UniProt & NIH Common Fund Data Resources
Find proteins for P62745 (Homo sapiens)
Explore P62745 
Go to UniProtKB:  P62745
PHAROS:  P62745
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62745
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nanobody B6
B, D
134Homo sapiensMutation(s): 0 
UniProt
Find proteins for A0A4E0W6L3 (Homo sapiens)
Explore A0A4E0W6L3 
Go to UniProtKB:  A0A4E0W6L3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4E0W6L3
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.84α = 90
b = 70.227β = 107.68
c = 71.212γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Database references