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- PDB-7p1t: Cryo-EM structure of encapsulin from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 7p1t
TitleCryo-EM structure of encapsulin from Mycobacterium tuberculosis
Components29 kDa antigen, Cfp29
KeywordsVIRUS LIKE PARTICLE / encapsulin / cfp29 / nanocompartment
Function / homologyType 1 encapsulin shell protein / Encapsulating protein for peroxidase / : / encapsulin nanocompartment / Hydrolases; Acting on peptide bonds (peptidases) / hydrolase activity / 29 kDa antigen, Cfp29
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.29 Å
AuthorsLewis, C.J. / Berger, C. / Ravelli, R.B.G.
Funding support Netherlands, 2items
OrganizationGrant numberCountry
Other governmentLHSM18067 Netherlands
Netherlands Organisation for Scientific Research (NWO)184.034.014 Netherlands
CitationJournal: To Be Published
Title: Encapsulins in mycobacteria: from single particle to in situ
Authors: Lewis, C.J. / Berger, C. / Gao, Y. / Lopez-Iglesias, C. / Peters, P.J. / Ravelli, R.B.G.
History
DepositionJul 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
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
AA: 29 kDa antigen, Cfp29
BA: 29 kDa antigen, Cfp29
CA: 29 kDa antigen, Cfp29
DA: 29 kDa antigen, Cfp29
EA: 29 kDa antigen, Cfp29
FA: 29 kDa antigen, Cfp29
GA: 29 kDa antigen, Cfp29
HA: 29 kDa antigen, Cfp29
IA: 29 kDa antigen, Cfp29
JA: 29 kDa antigen, Cfp29
KA: 29 kDa antigen, Cfp29
LA: 29 kDa antigen, Cfp29
MA: 29 kDa antigen, Cfp29
NA: 29 kDa antigen, Cfp29
OA: 29 kDa antigen, Cfp29
PA: 29 kDa antigen, Cfp29
QA: 29 kDa antigen, Cfp29
RA: 29 kDa antigen, Cfp29
SA: 29 kDa antigen, Cfp29
TA: 29 kDa antigen, Cfp29
UA: 29 kDa antigen, Cfp29
VA: 29 kDa antigen, Cfp29
WA: 29 kDa antigen, Cfp29
XA: 29 kDa antigen, Cfp29
YA: 29 kDa antigen, Cfp29
ZA: 29 kDa antigen, Cfp29
AB: 29 kDa antigen, Cfp29
BB: 29 kDa antigen, Cfp29
CB: 29 kDa antigen, Cfp29
DB: 29 kDa antigen, Cfp29
EB: 29 kDa antigen, Cfp29
FB: 29 kDa antigen, Cfp29
GB: 29 kDa antigen, Cfp29
HB: 29 kDa antigen, Cfp29


Theoretical massNumber of molelcules
Total (without water)1,731,80160
Polymers1,731,80160
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area261100 Å2
ΔGint-450 kcal/mol
Surface area567590 Å2
MethodPISA

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Components

#1: Protein ...
29 kDa antigen, Cfp29 / Bacteriocin / Linocin-M18


Mass: 28863.346 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria)
Gene: 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, ...Gene: 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
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: A0A045HTX8, Hydrolases; Acting on peptide bonds (peptidases)

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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: encapsulin shell from Mycobacterium tuberculosis / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.729 MDa / Experimental value: NO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: C41
Buffer solutionpH: 7
SpecimenConc.: 2.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 %

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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 magnification: 163000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 700 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1RELION3.1particle selection
2EPUimage acquisition
4GctfCTF correction
7PHENIX1.18.2model fitting
8Coot0.9.5model fitting
10PHENIX1.18.2model refinement
11Coot0.9.5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 89072
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 2.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57805 / Symmetry type: POINT
Atomic model buildingB value: 34.36 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: multiple
Atomic model buildingPDB-ID: 619G

619g


Accession code: 619G / Source name: PDB / Type: experimental model

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