6QGX

Crystal structure of E.coli BamA beta-barrel in complex with nanobody F7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Identification of conformation-selective nanobodies against the membrane protein insertase BamA by an integrated structural biology approach.

Kaur, H.Hartmann, J.B.Jakob, R.P.Zahn, M.Zimmermann, I.Maier, T.Seeger, M.A.Hiller, S.

(2019) J Biomol NMR 73: 375-384

  • DOI: 10.1007/s10858-019-00250-8
  • Primary Citation of Related Structures:  
    6QGW, 6QGX, 6QGY

  • PubMed Abstract: 
  • The insertase BamA is an essential protein of the bacterial outer membrane. Its 16-stranded transmembrane β-barrel contains a lateral gate as a key functional element. This gate is formed by the C-terminal half of the last β-strand. The BamA barrel was previously found to sample different conformations in aqueous solution, as well as different gate-open, gate-closed, and collapsed conformations in X-ray crystallography and cryo-electron microscopy structures ...

    The insertase BamA is an essential protein of the bacterial outer membrane. Its 16-stranded transmembrane β-barrel contains a lateral gate as a key functional element. This gate is formed by the C-terminal half of the last β-strand. The BamA barrel was previously found to sample different conformations in aqueous solution, as well as different gate-open, gate-closed, and collapsed conformations in X-ray crystallography and cryo-electron microscopy structures. Here, we report the successful identification of conformation-selective nanobodies that stabilize BamA in specific conformations. While the initial candidate generation and selection protocol was based on established alpaca immunization and phage display selection procedures, the final selection of nanobodies was enhanced by a solution NMR-based screening step to shortlist the targets for crystallization. In this way, three crystal structures of BamA-nanobody complexes were efficiently obtained, showing two types of nanobodies that indeed stabilized BamA in two different conformations, i.e., with open and closed lateral gate, respectively. Then, by correlating the structural data with high resolution NMR spectra, we could for the first time assign the BamA conformational solution ensemble to defined structural states. The new nanobodies will be valuable tools towards understanding the client insertion mechanism of BamA and towards developing improved antibiotics.


    Organizational Affiliation

    Biozentrum, University of Basel, 4056, Basel, Switzerland. sebastian.hiller@unibas.ch.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamAA411Escherichia coli O157:H7Mutation(s): 2 
Gene Names: bamAyaeTZ0188ECs0179
Membrane Entity: Yes 
UniProt
Find proteins for P0A942 (Escherichia coli O157:H7)
Explore P0A942 
Go to UniProtKB:  P0A942
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A942
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NanoF7B126Lama glamaMutation(s): 0 
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: 2.20 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.321α = 90
b = 80.335β = 90
c = 135.349γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-08-21
    Changes: Data collection, Database references