3EZJ

Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody.

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

(2009) Structure 17: 255-265

  • DOI: 10.1016/j.str.2008.11.011

  • PubMed Abstract: 
  • Secretins are among the largest bacterial outer membrane proteins known. Here we report the crystal structure of the periplasmic N-terminal domain of GspD (peri-GspD) from the type 2 secretion system (T2SS) secretin in complex with a nanobody, the VH ...

    Secretins are among the largest bacterial outer membrane proteins known. Here we report the crystal structure of the periplasmic N-terminal domain of GspD (peri-GspD) from the type 2 secretion system (T2SS) secretin in complex with a nanobody, the VHH domain of a heavy-chain camelid antibody. Two different crystal forms contained the same compact peri-GspD:nanobody heterotetramer. The nanobody contacts peri-GspD mainly via CDR3 and framework residues. The peri-GspD structure reveals three subdomains, with the second and third subdomains exhibiting the KH fold which also occurs in ring-forming proteins of the type 3 secretion system. The first subdomain of GspD is related to domains in phage tail proteins and outer membrane TonB-dependent receptors. A dodecameric peri-GspD model is proposed in which a solvent-accessible beta strand of the first subdomain interacts with secreted proteins and/or T2SS partner proteins by beta strand complementation.


    Organizational Affiliation

    Department of Biochemistry, Biomolecular Structure Center, University of Washington, Seattle, WA 98195, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
General secretion pathway protein GspD
A, C, E, G
241Escherichia coliMutation(s): 1 
Gene Names: gspD
Find proteins for Q707C1 (Escherichia coli)
Go to UniProtKB:  Q707C1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NANOBODY NBGSPD_7
B, D, F, H
126N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 98.520α = 90.00
b = 98.520β = 90.00
c = 402.100γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
SHELXDphasing
RESOLVEphasing
SHELXphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Type: Structure summary