3SYN | pdb_00003syn

Crystal structure of FlhF in complex with its activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free: 
    0.239 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Structural basis for the molecular evolution of SRP-GTPase activation by protein.

Bange, G.Kummerer, N.Grudnik, P.Lindner, R.Petzold, G.Kressler, D.Hurt, E.Wild, K.Sinning, I.

(2011) Nat Struct Mol Biol 18: 1376-1380

  • DOI: https://doi.org/10.1038/nsmb.2141
  • Primary Citation Related Structures: 
    3SYN

  • PubMed Abstract: 

    Small G proteins have key roles in signal transduction pathways. They are switched from the signaling 'on' to the non-signaling 'off' state when GTPase-activating proteins (GAPs) provide a catalytic residue. The ancient signal recognition particle (SRP)-type GTPases form GTP-dependent homo- and heterodimers and deviate from the canonical switch paradigm in that no GAPs have been identified. Here we show that the YlxH protein activates the SRP-GTPase FlhF. The crystal structure of the Bacillus subtilis FlhF-effector complex revealed that the effector does not contribute a catalytic residue but positions the catalytic machinery already present in SRP-GTPases. We provide a general concept that might also apply to the RNA-driven activation of the universally conserved, co-translational protein-targeting machinery comprising the SRP-GTPases Ffh and FtsY. Our study exemplifies the evolutionary transition from RNA- to protein-driven activation in SRP-GTPases and suggests that the current view on SRP-mediated protein targeting is incomplete.


  • Organizational Affiliation
    • Heidelberg University Biochemistry Center, Heidelberg, Germany. gert.bange@bzh.uni-heidelberg.de

Macromolecule Content 

  • Total Structure Weight: 148.76 kDa 
  • Atom Count: 9,010 
  • Modeled Residue Count: 1,096 
  • Deposited Residue Count: 1,276 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Flagellar biosynthesis protein flhF
A, B, C, D
296Bacillus subtilisMutation(s): 0 
Gene Names: flhFBSU16400
UniProt
Find proteins for Q01960 (Bacillus subtilis (strain 168))
Explore Q01960 
Go to UniProtKB:  Q01960
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ01960
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ATP-binding protein YlxH
E, F, G, H
23Bacillus subtilisMutation(s): 0 
UniProt
Find proteins for P40742 (Bacillus subtilis (strain 168))
Explore P40742 
Go to UniProtKB:  P40742
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40742
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
DA [auth D],
I [auth A],
Q [auth B],
W [auth C]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
CA [auth C]
GA [auth D]
HA [auth D]
AA [auth C],
BA [auth C],
CA [auth C],
GA [auth D],
HA [auth D],
IA [auth D],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
T [auth B],
U [auth B],
V [auth B],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
AF3

Query on AF3



Download:Ideal Coordinates CCD File
FA [auth D],
K [auth A],
S [auth B],
Y [auth C]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
EA [auth D],
J [auth A],
R [auth B],
X [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.06 Å
  • R-Value Free:  0.239 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.79α = 92.26
b = 63.36β = 100.96
c = 114.5γ = 94.25
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-11-09
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Database references
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description