8PYS

Cryo-EM structure of the DyP peroxidase-loaded encapsulin nanocompartment from Mycobacterium tuberculosis with icosahedral symmetry imposed.

• PDB DOI: https://doi.org/10.2210/pdb8PYS/pdb
• EM Map EMD-18031: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli DH5[alpha]
• Mutation(s): No 


• Deposited: 2023-07-26 Released: 2023-08-09 
• Deposition Author(s): Willmore, R., Woodward, J.D.
• Funding Organization(s): Global Challenges Research Fund

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

The 2.7 A resolution cryo-EM reconstruction of Mycobacterium tuberculosis encapsulin nanocompartment containing DyP peroxidase.

Willmore, R., Woodward, J.D.

To be published.

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: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,773.24 kDa 
• Atom Count: 122,040 
• Modelled Residue Count: 15,900 
• Deposited Residue Count: 16,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
29 kDa antigen CFP29	A, AA [auth a], AB [auth 0], B, BA [auth b], BB [auth 1], C, CA [auth c], CB [auth 2], D, DA [auth d], DB [auth 3], E, EA [auth e], EB [auth 4], F, FA [auth f], FB [auth 5], G, GA [auth g], GB [auth 6], H, HA [auth h], HB [auth 7], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	270	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: cfp29, Rv0798c
UniProt
Find proteins for I6WZG6 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6WZG6  Go to UniProtKB:  I6WZG6

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.0.
MODEL REFINEMENT	PHENIX	1.20.1.

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Willmore, R., Woodward, J.D.

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Funding Organization	Location	Grant Number
Global Challenges Research Fund	United Kingdom	--

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2024-07-24
  Changes: Data collection, Refinement description