[English] 日本語
Yorodumi
- PDB-7p1t: Cryo-EM structure of encapsulin from Mycobacterium tuberculosis -

+
Open data


ID or keywords:

Loading...

-
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 / Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / defense response to bacterium / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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)

-
Experimental details

-
Experiment

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

-
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 %

-
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)

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more