8XNB | pdb_00008xnb

Cryo-EM structure of Deinococcus radiodurans BamA

• PDB DOI: https://doi.org/10.2210/pdb8XNB/pdb
• EM Map EMD-38500: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2023-12-29 Released: 2025-01-15 
• Deposition Author(s): Qian, H.W., Wang, Z.Z.
• Funding Organization(s): Other private

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural insights into Deinococcus radiodurans BamA: extracellular loop diversity and its evolutionary implications

Wang, Z.Z., Xue, J.C., Wang, J.J., Yu, J.G., Qian, H.W., Yang, X.X.

(2024) JUSTC 54

• DOI: https://doi.org/10.52396/JUSTC-2024-0012

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 187.62 kDa 
• Atom Count: 5,580 
• Modeled Residue Count: 738 
• Deposited Residue Count: 1,756 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Outer membrane protein assembly factor BamA	A, B	878	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_0379 Membrane Entity: Yes
UniProt
Find proteins for Q9RXD5 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RXD5  Go to UniProtKB:  Q9RXD5

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-15 
Deposition Author(s): Qian, H.W., Wang, Z.Z.

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Funding Organization	Location	Grant Number
Other private	China	KY9100000034

Revision History  

• Version 1.0: 2025-01-15
  Type: Initial release
  
• Version 1.1: 2025-01-22
  Changes: Data collection, Database references, Structure summary
• Version 1.2: 2025-07-02
  Changes: Data collection