3CFI

Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nanobody-aided structure determination of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus.

Lam, A.Y.Pardon, E.Korotkov, K.V.Hol, W.G.Steyaert, J.

(2009) J.Struct.Biol. 166: 8-15

  • DOI: 10.1016/j.jsb.2008.11.008

  • PubMed Abstract: 
  • Pseudopilins form the central pseudopilus of the sophisticated bacterial type 2 secretion systems. The crystallization of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus was greatly accelerated by the use of nanobodies, which are the sma ...

    Pseudopilins form the central pseudopilus of the sophisticated bacterial type 2 secretion systems. The crystallization of the EpsI:EpsJ pseudopilin heterodimer from Vibrio vulnificus was greatly accelerated by the use of nanobodies, which are the smallest antigen-binding fragments derived from heavy-chain only camelid antibodies. Seven anti-EpsI:EpsJ nanobodies were generated and co-crystallization of EpsI:EpsJ nanobody complexes yielded several crystal forms very rapidly. In the structure solved, the nanobodies are arranged in planes throughout the crystal lattice, linking layers of EpsI:EpsJ heterodimers. The EpsI:EpsJ dimer observed confirms a right-handed architecture of the pseudopilus, but, compared to a previous structure of the EpsI:EpsJ heterodimer, EpsI differs 6 degrees in orientation with respect to EpsJ; one loop of EpsJ is shifted by approximately 5A due to interactions with the nanobody; and a second loop of EpsJ underwent a major change of 17A without contacts with the nanobody. Clearly, nanobodies accelerate dramatically the crystallization of recalcitrant protein complexes and can reveal conformational flexibility not observed before.


    Organizational Affiliation

    Department of Biochemistry, Biomolecular Structure Center, University of Washington, 1959 Pacific Ave. NE, HSC K-428, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Type II secretory pathway, pseudopilin EpsI
A, D, G, J
84Vibrio vulnificus (strain YJ016)Mutation(s): 0 
Find proteins for Q7MPZ1 (Vibrio vulnificus (strain YJ016))
Go to UniProtKB:  Q7MPZ1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Type II secretory pathway, PSEUDOPILIN EpsJ
B, E, H, K
164Vibrio vulnificus (strain YJ016)Mutation(s): 0 
Find proteins for Q7MPZ0 (Vibrio vulnificus (strain YJ016))
Go to UniProtKB:  Q7MPZ0
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Nanobody NBEPSIJ_11
C, F, I, L
116N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
B, E, H, K
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.58 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.229 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.720α = 96.54
b = 67.243β = 91.62
c = 128.255γ = 90.20
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PHASERphasing
XDSdata scaling
Blu-Icedata collection
MOSFLMdata reduction
RESOLVEphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-01-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance