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- PDB-7phm: Cryo-EM structure of Mycobacterium tuberculosis encapsulin -

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Basic information

Entry
Database: PDB / ID: 7phm
TitleCryo-EM structure of Mycobacterium tuberculosis encapsulin
Components29 kDa antigen CFP29
KeywordsSTRUCTURAL PROTEIN / Encapsulin / icosahedral / oxidative stress response
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / extracellular region / plasma membrane / Type 1 encapsulin shell protein
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsWoodward, J.D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Global Challenges Research FundST/R002754/1 United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of Mycobacterium tuberculosis encapsulin
Authors: Woodward, J.D.
History
DepositionAug 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
Z: 29 kDa antigen CFP29
A: 29 kDa antigen CFP29
B: 29 kDa antigen CFP29
C: 29 kDa antigen CFP29
D: 29 kDa antigen CFP29
E: 29 kDa antigen CFP29
F: 29 kDa antigen CFP29
G: 29 kDa antigen CFP29
H: 29 kDa antigen CFP29
I: 29 kDa antigen CFP29
J: 29 kDa antigen CFP29
K: 29 kDa antigen CFP29
L: 29 kDa antigen CFP29
M: 29 kDa antigen CFP29
N: 29 kDa antigen CFP29
O: 29 kDa antigen CFP29
P: 29 kDa antigen CFP29
Q: 29 kDa antigen CFP29
R: 29 kDa antigen CFP29
S: 29 kDa antigen CFP29
T: 29 kDa antigen CFP29
U: 29 kDa antigen CFP29
V: 29 kDa antigen CFP29
W: 29 kDa antigen CFP29
X: 29 kDa antigen CFP29
Y: 29 kDa antigen CFP29
a: 29 kDa antigen CFP29
b: 29 kDa antigen CFP29
c: 29 kDa antigen CFP29
d: 29 kDa antigen CFP29
e: 29 kDa antigen CFP29
f: 29 kDa antigen CFP29
g: 29 kDa antigen CFP29
h: 29 kDa antigen CFP29
i: 29 kDa antigen CFP29
j: 29 kDa antigen CFP29
k: 29 kDa antigen CFP29
l: 29 kDa antigen CFP29
m: 29 kDa antigen CFP29
n: 29 kDa antigen CFP29
o: 29 kDa antigen CFP29
p: 29 kDa antigen CFP29
q: 29 kDa antigen CFP29
r: 29 kDa antigen CFP29
s: 29 kDa antigen CFP29
t: 29 kDa antigen CFP29
u: 29 kDa antigen CFP29
v: 29 kDa antigen CFP29
w: 29 kDa antigen CFP29
x: 29 kDa antigen CFP29
y: 29 kDa antigen CFP29
z: 29 kDa antigen CFP29
0: 29 kDa antigen CFP29
1: 29 kDa antigen CFP29
2: 29 kDa antigen CFP29
3: 29 kDa antigen CFP29
4: 29 kDa antigen CFP29
5: 29 kDa antigen CFP29
6: 29 kDa antigen CFP29
7: 29 kDa antigen CFP29


Theoretical massNumber of molelcules
Total (without water)1,773,24460
Polymers1,773,24460
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein ...
29 kDa antigen CFP29 / Encapsulin


Mass: 29554.072 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: cfp29, Rv0798c / Plasmid: pET-28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): CodonPlus / References: UniProt: I6WZG6

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Empty encapsulin nanocompartment / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.73 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria) / Plasmid: pET-28a(+)
Buffer solutionpH: 7.4
Details: Eluted in: 50mM Tris-HCl, 350mM NaCl, 10mM Imidazol, 10% v/v glycerol at pH 7.4 and diluted 1:2 in distilled water.
Buffer component
IDConc.NameFormulaBuffer-ID
1175 mMsodium chlorideNaCl1
225 mMTRISC4H11NO31
3250 mMimidazolC3H4N21
45 % (v/v)glycerolC3H8O31
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: C-flat 2/2 holey carbon film supported by a standard copper TEM grid and coated with an ultrathin (2-3 nm) continuous carbon film.
Specimen supportDetails: Glow-discharged using an EMS100X in air: 25 mA at 20 Pa for 30 seconds.
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 45 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 14133
Details: Data collected in super-resolution mode at 0.53 A/pixel and down-sampled during motion correction to 1.06 A/pixel.
Image scansWidth: 11520 / Height: 8184

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1RELION3.1.1particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7UCSF Chimera1.12model fitting
9RELION3.1.1initial Euler assignment
10RELION3.1.1final Euler assignment
11RELION3.1.1classification
12RELION3.1.13D reconstruction
19ISOLDE1.2model refinement
20PHENIX1.13model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2000000
Details: 2D class averages were produced using Relion from 1000 manually-picked particles. These were then used as picking templates.
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1000000 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Details: Model was generated ab initio using Buccaneer within the CCPEM package and manually corrected using Coot before being refined using Isolde within ChimeraX and Phenix Real Space Refinement ...Details: Model was generated ab initio using Buccaneer within the CCPEM package and manually corrected using Coot before being refined using Isolde within ChimeraX and Phenix Real Space Refinement within the CCPEM package.

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