8DFU

Cryo-EM structure of conjugation pili from Aeropyrum pernix

  • Classification: PROTEIN FIBRIL
  • Organism(s): Aeropyrum pernix
  • Mutation(s): No 
  • Membrane Protein: Yes  OPM

  • Deposited: 2022-06-22 Released: 2023-03-22 
  • Deposition Author(s): Beltran, L.C., Egelman, E.H.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Archaeal DNA-import apparatus is homologous to bacterial conjugation machinery.

Beltran, L.C.Cvirkaite-Krupovic, V.Miller, J.Wang, F.Kreutzberger, M.A.B.Patkowski, J.B.Costa, T.R.D.Schouten, S.Levental, I.Conticello, V.P.Egelman, E.H.Krupovic, M.

(2023) Nat Commun 14: 666-666

  • DOI: https://doi.org/10.1038/s41467-023-36349-8
  • Primary Citation of Related Structures:  
    8DFT, 8DFU, 8EXH

  • PubMed Abstract: 

    Conjugation is a major mechanism of horizontal gene transfer promoting the spread of antibiotic resistance among human pathogens. It involves establishing a junction between a donor and a recipient cell via an extracellular appendage known as the mating pilus. In bacteria, the conjugation machinery is encoded by plasmids or transposons and typically mediates the transfer of cognate mobile genetic elements. Much less is known about conjugation in archaea. Here, we determine atomic structures by cryo-electron microscopy of three conjugative pili, two from hyperthermophilic archaea (Aeropyrum pernix and Pyrobaculum calidifontis) and one encoded by the Ti plasmid of the bacterium Agrobacterium tumefaciens, and show that the archaeal pili are homologous to bacterial mating pili. However, the archaeal conjugation machinery, known as Ced, has been 'domesticated', that is, the genes for the conjugation machinery are encoded on the chromosome rather than on mobile genetic elements, and mediates the transfer of cellular DNA.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pilin protein84Aeropyrum pernixMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A401HBH5 (Aeropyrum pernix)
Explore A0A401HBH5 
Go to UniProtKB:  A0A401HBH5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A401HBH5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RHR (Subject of Investigation/LOI)
Query on RHR

Download Ideal Coordinates CCD File 
AB [auth H]
AC [auth U]
BB [auth H]
BC [auth U]
CB [auth I]
AB [auth H],
AC [auth U],
BB [auth H],
BC [auth U],
CB [auth I],
CC [auth V],
DB [auth I],
DC [auth V],
EA [auth B],
EB [auth J],
EC [auth W],
FA [auth B],
FB [auth J],
FC [auth W],
GA [auth A],
GB [auth K],
GC [auth X],
HA [auth A],
HB [auth K],
HC [auth X],
IA [auth A],
IB [auth L],
IC [auth Y],
JA [auth C],
JB [auth L],
JC [auth Y],
KA [auth C],
KB [auth M],
KC [auth Z],
LA [auth C],
LB [auth M],
LC [auth Z],
MA [auth C],
MB [auth N],
NA [auth D],
NB [auth N],
OA [auth D],
OB [auth O],
PA [auth D],
PB [auth O],
QA [auth D],
QB [auth P],
RA [auth E],
RB [auth P],
SA [auth E],
SB [auth Q],
TA [auth E],
TB [auth Q],
UA [auth E],
UB [auth R],
VA [auth F],
VB [auth R],
WA [auth F],
WB [auth S],
XA [auth F],
XB [auth S],
YA [auth G],
YB [auth T],
ZA [auth G],
ZB [auth T]
(2S)-3-{[(3R,7S,11S,15S)-3,7,11,15,19-pentamethylicosyl]oxy}-2-{[(2R,6S,10S,14R)-2,6,10,14,18-pentamethylnonadecyl]oxy}propyl dihydrogen phosphate
C52 H107 O6 P
LOOIOWMHQRRBDQ-UYUJORPFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.44 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM122510

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release