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: 2.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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This is version 1.3 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
  • Primary Citation of Related Structures:  
    3EZJ

  • 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 VHH domain of a heavy-chain camelid antibody ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
General secretion pathway protein GspDA,
B [auth C],
C [auth E],
D [auth G]
241Escherichia coli ETEC H10407Mutation(s): 1 
Gene Names: gspD
UniProt
Find proteins for Q707C1 (Escherichia coli)
Explore Q707C1 
Go to UniProtKB:  Q707C1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ707C1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NANOBODY NBGSPD_7E [auth B],
F [auth D],
G [auth F],
H
126Lama glamaMutation(s): 0 
Gene Names: NBGSPD_7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.52α = 90
b = 98.52β = 90
c = 402.1γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXphasing
RESOLVEphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SHELXDphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2018-01-24
    Changes: Structure summary
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations