2XKV

Atomic Model of the SRP-FtsY Early Conformation

• PDB DOI: https://doi.org/10.2210/pdb2XKV/pdb
• EM Map EMD-1762: EMDB EMDataResource
• NAKB: 2XKV

• Classification: PROTEIN TRANSPORT
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-07-13 Released: 2010-12-15 
• Deposition Author(s): Estrozi, L.F., Boehringer, D., Shan, S.-o., Ban, N., Schaffitzel, C.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 13.5 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Cryo-Em Structure of the E. Coli Translating Ribosome in Complex with Srp and its Receptor.

Estrozi, L.F., Boehringer, D., Shan, S.-O., Ban, N., Schaffitzel, C.

(2011) Nat Struct Mol Biol 18: 88

• PubMed: 21151118 
• DOI: https://doi.org/10.1038/nsmb.1952
• Primary Citation of Related Structures:  
  2XKV


• PubMed Abstract: 
  

  We report the 'early' conformation of the Escherichia coli signal recognition particle (SRP) and its receptor FtsY bound to the translating ribosome, as determined by cryo-EM. FtsY binds to the tetraloop of the SRP RNA, whereas the NG domains of the SRP protein and FtsY interact weakly in this conformation. Our results suggest that optimal positioning of the SRP RNA tetraloop and the Ffh NG domain leads to FtsY recruitment.

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Organizational Affiliation: 

European Molecular Biology Laboratory, Grenoble Outstation, Grenoble, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.29 kDa 
• Atom Count: 6,620 
• Modelled Residue Count: 698 
• Deposited Residue Count: 780 
• Unique protein chains: 3
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIGNAL RECOGNITION PARTICLE PROTEIN	A	294	Escherichia coli	Mutation(s): 0  EC: 3.6.5.4
UniProt
Find proteins for O07347 (Thermus aquaticus) Explore O07347  Go to UniProtKB:  O07347

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SIGNAL RECOGNITION PARTICLE PROTEIN	C	69	Escherichia coli	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
CELL DIVISION PROTEIN FTSY	D	303	Escherichia coli	Mutation(s): 0  EC: 3.6.5.4
UniProt
Find proteins for P83749 (Thermus aquaticus) Explore P83749  Go to UniProtKB:  P83749

Entity ID: 2
Molecule	Chains	Length	Organism	Image
4.5S RNA	B	114	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 13.5 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-15 
Deposition Author(s): Estrozi, L.F., Boehringer, D., Shan, S.-o., Ban, N., Schaffitzel, C.

Revision History  

• Version 1.0: 2010-12-15
  Type: Initial release
  
• Version 1.1: 2011-08-31
  Changes: Database references, Version format compliance
• Version 1.2: 2013-03-20
  Changes: Other, Refinement description
• Version 2.0: 2017-08-23
  Changes: Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Refinement description