5N8O | pdb_00005n8o

Cryo EM structure of the conjugative relaxase TraI of the F/R1 plasmid system

• PDB DOI: https://doi.org/10.2210/pdb5N8O/pdb
• EM Map EMD-3601: EMDB EMDataResource
• NAKB: 5N8O

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


• Deposited: 2017-02-23 Released: 2017-05-03 
• Deposition Author(s): Ilangovan, A., Zanetti, G., Waksman, G.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM Structure of a Relaxase Reveals the Molecular Basis of DNA Unwinding during Bacterial Conjugation

Ilangovan, A., Kay, C.W.M., Roier, S., El Mkami, H., Salvadori, E., Zechner, E.L., Zanetti, G., Waksman, G.

(2017) Cell 169: 708-721.e12

• PubMed: 28457609 
• DOI: https://doi.org/10.1016/j.cell.2017.04.010
• Primary Citation Related Structures: 
  5N8O


• PubMed Abstract: 
  

  Relaxases play essential roles in conjugation, the main process by which bacteria exchange genetic material, notably antibiotic resistance genes. They are bifunctional enzymes containing a trans-esterase activity, which is responsible for nicking the DNA strand to be transferred and for covalent attachment to the resulting 5'-phosphate end, and a helicase activity, which is responsible for unwinding the DNA while it is being transported to a recipient cell. Here we show that these two activities are carried out by two conformers that can both load simultaneously on the origin of transfer DNA. We solve the structure of one of these conformers by cryo electron microscopy to near-atomic resolution, elucidating the molecular basis of helicase function by relaxases and revealing insights into the mechanistic events taking place in the cell prior to substrate transport during conjugation.

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Organizational Affiliation: 
• Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, UK.
Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK; London Centre for Nanotechnology, University College London, 17-19 Gordon Street, London WC1H 0AH, UK.
Institute of Molecular Biosciences, University of Graz, BioTechMed-Graz, Humboldtstrasse 50, 8010 Graz, Austria.
School of Physics and Astronomy, University of St Andrews, St Andrews KY16 9SS, UK.
Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, UK. Electronic address: [e-mail].
Institute of Structural and Molecular Biology, Birkbeck, Malet Street, London WC1E 7HX, UK; Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, UK. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 198.64 kDa 
• Atom Count: 11,362 
• Modeled Residue Count: 1,450 
• Deposited Residue Count: 1,778 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA helicase I	A	1,756	Escherichia coli	Mutation(s): 0  Gene Names: traI EC: 5.6.2.3 (UniProt), 5.6.2 (UniProt)
UniProt
Find proteins for Q6TDU5 (Escherichia coli) Explore Q6TDU5  Go to UniProtKB:  Q6TDU5

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')	B [auth C]	22	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.0
MODEL REFINEMENT	PHENIX	1.11.1

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Ilangovan, A., Zanetti, G., Waksman, G.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	--

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references
• Version 1.2: 2017-05-17
  Changes: Database references
• Version 1.3: 2017-05-31
  Changes: Structure summary
• Version 1.4: 2017-06-28
  Changes: Database references
• Version 1.5: 2017-08-30
  Changes: Data collection, Experimental preparation
• Version 1.6: 2019-12-11
  Changes: Other
• Version 1.7: 2020-11-18
  Changes: Data collection
• Version 1.8: 2024-05-15
  Changes: Data collection, Database references