7P1T

Cryo-EM structure of encapsulin from Mycobacterium tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb7P1T/pdb
• EM Map EMD-13164: EMDB EMDataResource

• Classification: VIRUS LIKE PARTICLE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-07-02 Released: 2022-07-13 
• Deposition Author(s): Lewis, C.J., Berger, C., Ravelli, R.B.G.
• Funding Organization(s): Other government, Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Encapsulins in mycobacteria: from single particle to in situ

Lewis, C.J., Berger, C., Gao, Y., Lopez-Iglesias, C., Peters, P.J., Ravelli, R.B.G.

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 PISA (software)

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 1,731.8 kDa 
• Atom Count: 122,040 
• Modelled Residue Count: 15,900 
• Deposited Residue Count: 15,900 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
29 kDa antigen, Cfp29	A, AA, AB, B, BA, BB, C, CA, CB, D, DA, DB, E, EA, EB, F, FA, FB, G, GA, GB, H, HA, HB, I, IA, J, JA, K, KA, L, LA, M, MA, N, NA, O, OA, P, PA, Q, QA, R, RA, S, SA, T, TA, U, UA, V, VA, W, WA, X, XA, Y, YA, Z, ZA	265	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names:  cfp29, lin, C0094_04325, CAB90_00906, DSI38_23045, E5M05_20280, E5M52_19875, E5M78_19835, ERS007661_02029, ERS007665_01536, ERS007679_03499, ERS007688_03248, ERS007741_01530, ERS013471_03708, ERS023446_03804, ERS027659_01280, ERS094182_03983, F6W99_03480, FRD82_02930, GCL30_20955, SAMEA2683035_02949 EC: 3.4
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: 2.29 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.18.2
MODEL REFINEMENT	Coot	0.9.5

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-07-13 
Deposition Author(s): Lewis, C.J., Berger, C., Ravelli, R.B.G.

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Funding Organization	Location	Grant Number
Other government	Netherlands	LHSM18067
Netherlands Organisation for Scientific Research (NWO)	Netherlands	184.034.014

Revision History  

• Version 1.0: 2022-07-13
  Type: Initial release
  
• Version 1.1: 2024-07-17
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary