2CNW

GDPALF4 complex of the SRP GTPases Ffh and FtsY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of a Gdp:Alf(4) Complex of the Srp Gtpases Ffh and Ftsy, and Identification of a Peripheral Nucleotide Interaction Site.

Focia, P.J.Gawronski-Salerno, J.Coon V, J.S.Freymann, D.M.

(2006) J Mol Biol 360: 631

  • DOI: 10.1016/j.jmb.2006.05.031
  • Primary Citation of Related Structures:  
    2CNW

  • PubMed Abstract: 
  • The signal recognition particle (SRP) GTPases Ffh and FtsY play a central role in co-translational targeting of proteins, assembling in a GTP-dependent manner to generate the SRP targeting complex at the membrane. A suite of residues in FtsY have been identified that are essential for the hydrolysis of GTP that accompanies disengagement ...

    The signal recognition particle (SRP) GTPases Ffh and FtsY play a central role in co-translational targeting of proteins, assembling in a GTP-dependent manner to generate the SRP targeting complex at the membrane. A suite of residues in FtsY have been identified that are essential for the hydrolysis of GTP that accompanies disengagement. We have argued previously on structural grounds that this region mediates interactions that serve to activate the complex for disengagement and term it the activation region. We report here the structure of a complex of the SRP GTPases formed in the presence of GDP:AlF4. This complex accommodates the putative transition-state analog without undergoing significant change from the structure of the ground-state complex formed in the presence of the GTP analog GMPPCP. However, small shifts that do occur within the shared catalytic chamber may be functionally important. Remarkably, an external nucleotide interaction site was identified at the activation region, revealed by an unexpected contaminating GMP molecule bound adjacent to the catalytic chamber. This site exhibits conserved sequence and structural features that suggest a direct interaction with RNA plays a role in regulating the activity of the SRP targeting complex.


    Organizational Affiliation

    Department of Molecular Pharmacology and Biological Chemistry, Feinberg School of Medicine, Northwestern University, 303 E. Chicago Ave., Chicago, IL 60611, USA. focia@northwestern.edu



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SIGNAL RECOGNITION PARTICLE PROTEINA, B, C294Thermus aquaticusMutation(s): 0 
Gene Names: ffh
UniProt
Find proteins for O07347 (Thermus aquaticus)
Explore O07347 
Go to UniProtKB:  O07347
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO07347
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CELL DIVISION PROTEIN FTSYD, E, F284Thermus aquaticusMutation(s): 0 
Gene Names: ftsY
UniProt
Find proteins for P83749 (Thermus aquaticus)
Explore P83749 
Go to UniProtKB:  P83749
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83749
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
G [auth A],
J [auth B],
M [auth C],
P [auth D],
T [auth E],
G [auth A],
J [auth B],
M [auth C],
P [auth D],
T [auth E],
X [auth F]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
5GP
Query on 5GP

Download Ideal Coordinates CCD File 
AA [auth F],
S [auth D],
W [auth E]
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
ALF
Query on ALF

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B],
O [auth C],
R [auth D],
V [auth E],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
V [auth E],
Z [auth F]
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
U [auth E],
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
U [auth E],
Y [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.186 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 188.686α = 90
b = 188.686β = 90
c = 44.588γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance