3NKV

Crystal structure of Rab1b covalently modified with AMP at Y77

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

The Legionella effector protein DrrA AMPylates the membrane traffic regulator Rab1b.

Muller, M.P., Peters, H., Blumer, J., Blankenfeldt, W., Goody, R.S., Itzen, A.

(2010) Science 329: 946-949

  • DOI: 10.1126/science.1192276
  • Primary Citation of Related Structures:  
    3NKU, 3NKV

  • PubMed Abstract: 

    • In the course of Legionnaires' disease, the bacterium Legionella pneumophila affects the intracellular vesicular trafficking of infected eukaryotic cells by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole ...

    In the course of Legionnaires' disease, the bacterium Legionella pneumophila affects the intracellular vesicular trafficking of infected eukaryotic cells by recruiting the small guanosine triphosphatase (GTPase) Rab1 to the cytosolic face of the Legionella-containing vacuole. In order to accomplish this, the Legionella protein DrrA contains a specific guanine nucleotide exchange activity for Rab1 activation that exchanges guanosine triphosphate (GTP) for guanosine diphosphate on Rab1. We found that the amino-terminal domain of DrrA possesses adenosine monophosphorylation (AMPylation) activity toward the switch II region of Rab1b, leading to posttranslational covalent modification of tyrosine 77. AMPylation of switch II by DrrA restricts the access of GTPase activating proteins, thereby rendering Rab1b constitutively active.

    Organizational Affiliation: 

    Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, NRW, 44227, Germany.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ras-related protein Rab-1BA, B175Homo sapiensMutation(s): 0 
Gene Names: RAB1B, RAB1B_HUMAN
EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0U4 (Homo sapiens)
Explore Q9H0U4 
Go to UniProtKB:  Q9H0U4
PHAROS:  Q9H0U4
GTEx:  ENSG00000174903 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0U4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]		PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N		 Ligand Interaction
AMP
Query on AMP
Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]		ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N		 Ligand Interaction
BA
Query on BA
Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]		BARIUM ION
Ba
XDFCIPNJCBUZJN-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.97α = 90
b = 100.589β = 102.43
c = 45.071γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-08-23
    Changes: Data collection