9CN0 | pdb_00009cn0

The cryo-EM structure of BamADE subcomplex from Neisseria gonorrhoeae


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural insights into outer membrane protein biogenesis in pathogenic Neisseria.

Billings, E.Fan, Z.Sooreshjani, M.A.Gumbart, J.C.Noinaj, N.

(2025) Structure 33: 1893

  • DOI: https://doi.org/10.1016/j.str.2025.08.009
  • Primary Citation of Related Structures:  
    9CMW, 9CN0, 9CN1

  • PubMed Abstract: 

    N. gonorrhoeae (Ngo) causes the sexually transmitted infection gonorrhea with ∼106 million infections worldwide annually. Ngo infections can result in an increased risk of acquiring HIV, infertility, and blindness. To combat Ngo infections, we report the cryoelectron microscopy (cryo-EM) structure of the Ngo β-barrel assembly machinery (NgBAM), which is responsible for the biogenesis of β-barrel outer membrane proteins (OMPs). NgBAM was observed in an inward-open state; however, the polypeptide transport-associated (POTRA) domains more closely match those found in the outward-open state in E. coli β-barrel assembly machinery (BAM). The barrel seam of NgBamA consists of partial pairing of strand β1 with β16; no outward-open state of NgBAM was observed. Molecular dynamics (MD) simulations reveal unique overall dynamics and interplay between the POTRA domains of NgBamA and NgBamD. We propose that in Ngo, initial recognition occurs in the inward-open state where the last strand of the OMP partially pairs with β1 of NgBamA and must compete off β16.


  • Organizational Affiliation
    • Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA793Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: bamANGO_1801
UniProt
Find proteins for Q5F5W8 (Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090))
Explore Q5F5W8 
Go to UniProtKB:  Q5F5W8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5F5W8
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamDB [auth D]272Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: bamDcomL
UniProt
Find proteins for Q50985 (Neisseria gonorrhoeae)
Explore Q50985 
Go to UniProtKB:  Q50985
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ50985
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamEC [auth E]140Neisseria gonorrhoeaeMutation(s): 0 
Gene Names: smpAbamENCTC11421_03635WHOF_00597WHOF_02071
UniProt
Find proteins for A0A1D3EW25 (Neisseria gonorrhoeae)
Explore A0A1D3EW25 
Go to UniProtKB:  A0A1D3EW25
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1D3EW25
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC3.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States909066
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM132024
Simons FoundationUnited StatesSF349247
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129539
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127884

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release
  • Version 1.1: 2025-09-10
    Changes: Data collection, Database references
  • Version 1.2: 2025-09-17
    Changes: Data collection, Database references
  • Version 1.3: 2025-11-19
    Changes: Data collection, Database references