9BI0 | pdb_00009bi0

Streptomyces griseus Family 2B encapsulin shell with 2-methylisoborneol synthase cargo in 20 mM cAMP


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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Literature

The biosynthesis of the odorant 2-methylisoborneol is compartmentalized inside a protein shell.

Andreas, M.P.Giessen, T.W.

(2024) Nat Commun 15: 9715-9715

  • DOI: https://doi.org/10.1038/s41467-024-54175-4
  • Primary Citation Related Structures: 
    9BHU, 9BHV, 9BI0

  • PubMed Abstract: 

    Terpenoids are the largest class of natural products, found across all domains of life. One of the most abundant bacterial terpenoids is the volatile odorant 2-methylisoborneol (2-MIB), partially responsible for the earthy smell of soil and musty taste of contaminated water. Many bacterial 2-MIB biosynthetic gene clusters were thought to encode a conserved transcription factor, named EshA in the model soil bacterium Streptomyces griseus. Here, we revise the function of EshA, now referred to as Sg Enc, and show that it is a Family 2B encapsulin shell protein. Using cryo-electron microscopy, we find that Sg Enc forms an icosahedral protein shell and encapsulates 2-methylisoborneol synthase (2-MIBS) as a cargo protein. Sg Enc contains a cyclic adenosine monophosphate (cAMP) binding domain (CBD)-fold insertion and a unique metal-binding domain, both displayed on the shell exterior. We show that Sg Enc CBDs do not bind cAMP. We find that 2-MIBS cargo loading is mediated by an N-terminal disordered cargo-loading domain and that 2-MIBS activity and Sg Enc shell structure are not modulated by cAMP. Our work redefines the function of EshA and establishes Family 2B encapsulins as cargo-loaded protein nanocompartments involved in secondary metabolite biosynthesis.


  • Organizational Affiliation
    • Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.

Macromolecule Content 

  • Total Structure Weight: 52.05 kDa 
  • Atom Count: 3,100 
  • Modeled Residue Count: 395 
  • Deposited Residue Count: 470 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleotide-binding protein470Streptomyces griseus subsp. griseusMutation(s): 0 
Gene Names: mmpI_1NCTC13033_02226
UniProt
Find proteins for Q54255 (Streptomyces griseus)
Explore Q54255 
Go to UniProtKB:  Q54255
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ54255
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.93 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.0+231114
MODEL REFINEMENTCoot8.9.1
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM133325

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release