5O74

Crystal structure of human Rab1b covalently bound to the GEF domain of DrrA/SidM from Legionella pneumophila in the presence of GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Proximity-Triggered Covalent Stabilization of Low-Affinity Protein Complexes In Vitro and In Vivo.

Cigler, M.Muller, T.G.Horn-Ghetko, D.von Wrisberg, M.K.Fottner, M.Goody, R.S.Itzen, A.Muller, M.P.Lang, K.

(2017) Angew Chem Int Ed Engl 56: 15737-15741

  • DOI: 10.1002/anie.201706927
  • Primary Citation of Related Structures:  
    5O74

  • PubMed Abstract: 
  • The characterization of low-affinity protein complexes is challenging due to their dynamic nature. Here, we present a method to stabilize transient protein complexes in vivo by generating a covalent and conformationally flexible bridge between the interaction partners ...

    The characterization of low-affinity protein complexes is challenging due to their dynamic nature. Here, we present a method to stabilize transient protein complexes in vivo by generating a covalent and conformationally flexible bridge between the interaction partners. A highly active pyrrolysyl tRNA synthetase mutant directs the incorporation of unnatural amino acids bearing bromoalkyl moieties (BrCnK) into proteins. We demonstrate for the first time that low-affinity protein complexes between BrCnK-containing proteins and their binding partners can be stabilized in vivo in bacterial and mammalian cells. Using this approach, we determined the crystal structure of a transient GDP-bound complex between a small G-protein and its nucleotide exchange factor. We envision that this approach will prove valuable as a general tool for validating and characterizing protein-protein interactions in vitro and in vivo.


    Organizational Affiliation

    Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Group of Synthetic Biochemistry, Technical University of Munich, Institute for Advanced Study, Lichtenbergstr. 4, 85748, Garching, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Multifunctional virulence effector protein DrrAA, C, E, G, I, K197Legionella pneumophilaMutation(s): 1 
Gene Names: drrAsidM
EC: 2.7.7
UniProt
Find proteins for Q29ST3 (Legionella pneumophila)
Explore Q29ST3 
Go to UniProtKB:  Q29ST3
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-1BB, D, F, H, J, L180Homo sapiensMutation(s): 1 
Gene Names: RAB1B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0U4 (Homo sapiens)
Explore Q9H0U4 
Go to UniProtKB:  Q9H0U4
PHAROS:  Q9H0U4
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.230 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.91α = 114.61
b = 87.45β = 97.69
c = 93.17γ = 100.74
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1035, grant B10
German Research FoundationGermanyGRK1721, grant C4
Center for Integrated Protein Science MunichGermanyCIPSM
German Research FoundationGermanySFB 642, grant A4

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 2.0: 2017-12-06
    Changes: Database references, Polymer sequence