4C7O | pdb_00004c7o

The structural basis of FtsY recruitment and GTPase activation by SRP RNA

• PDB DOI: https://doi.org/10.2210/pdb4C7O/pdb
• NAKB: 4C7O

• Classification: NUCLEAR PROTEIN/RNA
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-23 Released: 2013-11-20 
• Deposition Author(s): Voigts-Hoffmann, F., Schmitz, N., Shen, K., Shan, S.O., Ataide, S.F., Ban, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

The Structural Basis of Ftsy Recruitment and Gtpase Activation by Srp RNA

Voigts-Hoffmann, F., Schmitz, N., Shen, K., Shan, S.O., Ataide, S.F., Ban, N.

(2013) Mol Cell 52: 643

• PubMed: 24211265 
• DOI: https://doi.org/10.1016/j.molcel.2013.10.005
• Primary Citation Related Structures: 
  4C7O


• PubMed Abstract: 
  

  The universally conserved signal recognition particle (SRP) system mediates the targeting of membrane proteins to the translocon in a multistep process controlled by GTP hydrolysis. Here we present the 2.6 Å crystal structure of the GTPase domains of the E. coli SRP protein (Ffh) and its receptor (FtsY) in complex with the tetraloop and the distal region of SRP-RNA, trapped in the activated state in presence of GDP:AlF4. The structure reveals the atomic details of FtsY recruitment and, together with biochemical experiments, pinpoints G83 as the key RNA residue that stimulates GTP hydrolysis. Insertion of G83 into the FtsY active site orients a single glutamate residue provided by Ffh (E277), triggering GTP hydrolysis and complex disassembly at the end of the targeting cycle. The complete conservation of the key residues of the SRP-RNA and the SRP protein implies that the suggested chemical mechanism of GTPase activation is applicable across all kingdoms.

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Organizational Affiliation: 
• ETH Zurich (Swiss Federal Institute of Technology), Institute of Molecular Biology and Biophysics, Zürich 8093, Switzerland.
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address: [e-mail].
University of Sydney, School of Molecular Bioscience, Sydney, NSW 2006, Australia. Electronic address: [e-mail].
ETH Zurich (Swiss Federal Institute of Technology), Institute of Molecular Biology and Biophysics, Zürich 8093, Switzerland. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 143.56 kDa 
• Atom Count: 10,374 
• Modeled Residue Count: 1,186 
• Deposited Residue Count: 1,200 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIGNAL RECOGNITION PARTICLE PROTEIN	A, C	298	Escherichia coli K-12	Mutation(s): 0  EC: 3.6.5.4
UniProt
Find proteins for P0AGD7 (Escherichia coli (strain K12)) Explore P0AGD7  Go to UniProtKB:  P0AGD7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY	B, D	278	Escherichia coli K-12	Mutation(s): 0  EC: 3.6.5.4
UniProt
Find proteins for P10121 (Escherichia coli (strain K12)) Explore P10121  Go to UniProtKB:  P10121

Entity ID: 3
Molecule	Chains	Length	Organism	Image
SRP RNA	E	48	Escherichia coli K-12

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	H [auth A], K [auth B], N [auth C], Q [auth D], R [auth D]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
ALF	F [auth A], I [auth B], L [auth C], O [auth D]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
MG	G [auth A], J [auth B], M [auth C], P [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.226 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.72	α = 90
b = 166.33	β = 90
c = 154.59	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-20 
Deposition Author(s): Voigts-Hoffmann, F., Schmitz, N., Shen, K., Shan, S.O., Ataide, S.F., Ban, N.

Revision History  

• Version 1.0: 2013-11-20
  Type: Initial release
  
• Version 1.1: 2014-01-08
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description