7KQ5 | pdb_00007kq5

Cryo-EM structure of a thermostable encapsulin from T. maritima

• PDB DOI: https://doi.org/10.2210/pdb7KQ5/pdb
• EM Map EMD-22992: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-11-13 Released: 2021-04-28 
• Deposition Author(s): Wiryaman, T.I., Toor, N.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of a thermostable bacterial nanocompartment.

Wiryaman, T., Toor, N.

(2021) IUCrJ 8: 342-350

• PubMed: 33953921 
• DOI: https://doi.org/10.1107/S2052252521001949
• Primary Citation Related Structures: 
  7KQ5


• PubMed Abstract: 
  

  Protein nanocompartments are widespread in bacteria and archaea, but their functions are not yet well understood. Here, the cryo-EM structure of a nanocompartment from the thermophilic bacterium Thermotoga maritima is reported at 2.0 Å resolution. The high resolution of this structure shows that interactions in the E-loop domain may be important for the thermostability of the nanocompartment assembly. Also, the channels at the fivefold axis, threefold axis and dimer interface are assessed for their ability to transport iron. Finally, an unexpected flavin ligand was identified on the exterior of the shell, indicating that this nanocompartment may also play a direct role in iron metabolism.

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Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Homo 60-mer - A60 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 30.97 kDa 
• Atom Count: 2,331 
• Modeled Residue Count: 265 
• Deposited Residue Count: 265 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maritimacin	A	265	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: TM_0785 EC: 3.4
UniProt
Find proteins for Q9WZP2 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WZP2  Go to UniProtKB:  Q9WZP2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1
MODEL REFINEMENT	PHENIX	1.18.2

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Wiryaman, T.I., Toor, N.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM123275
National Institutes of Health/Office of the Director	United States	2T32GM007240
National Institutes of Health/Office of the Director	United States	U24GM129547

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2021-05-12
  Changes: Data collection, Database references
• Version 1.2: 2021-05-19
  Changes: Database references
• Version 1.3: 2024-03-06
  Changes: Data collection, Database references, Derived calculations, Refinement description