[English] 日本語
Yorodumi
- PDB-8ika: Cryo-EM structure of the encapsulin shell from Mycobacterium tube... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ika
TitleCryo-EM structure of the encapsulin shell from Mycobacterium tuberculosis
ComponentsType 1 encapsulin shell protein
KeywordsVIRUS LIKE PARTICLE / CFP-29 / Mycobacterium tuberculosis / cryo-EM / encapsulin
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 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsDu, Z. / Lai, Y. / Gao, Y. / Rao, Z. / Gong, H.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81520108019 China
National Natural Science Foundation of China (NSFC)32100976 China
National Natural Science Foundation of China (NSFC)82222042 China
CitationJournal: To Be Published
Title: Structure of mycobacterium tuberculosis encapsulin
Authors: Du, Z. / Lai, Y. / Gao, Y. / Rao, Z. / Gong, H.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A1: Type 1 encapsulin shell protein
A2: Type 1 encapsulin shell protein
A3: Type 1 encapsulin shell protein
A4: Type 1 encapsulin shell protein
A5: Type 1 encapsulin shell protein
A6: Type 1 encapsulin shell protein
A7: Type 1 encapsulin shell protein
A8: Type 1 encapsulin shell protein
A9: Type 1 encapsulin shell protein
AA: Type 1 encapsulin shell protein
AB: Type 1 encapsulin shell protein
AC: Type 1 encapsulin shell protein
AD: Type 1 encapsulin shell protein
AE: Type 1 encapsulin shell protein
AF: Type 1 encapsulin shell protein
AG: Type 1 encapsulin shell protein
AH: Type 1 encapsulin shell protein
AI: Type 1 encapsulin shell protein
AJ: Type 1 encapsulin shell protein
AK: Type 1 encapsulin shell protein
AL: Type 1 encapsulin shell protein
AM: Type 1 encapsulin shell protein
AN: Type 1 encapsulin shell protein
AO: Type 1 encapsulin shell protein
AP: Type 1 encapsulin shell protein
AQ: Type 1 encapsulin shell protein
AR: Type 1 encapsulin shell protein
AS: Type 1 encapsulin shell protein
AT: Type 1 encapsulin shell protein
AU: Type 1 encapsulin shell protein
AV: Type 1 encapsulin shell protein
AW: Type 1 encapsulin shell protein
AX: Type 1 encapsulin shell protein
AY: Type 1 encapsulin shell protein
AZ: Type 1 encapsulin shell protein
Aa: Type 1 encapsulin shell protein
Ab: Type 1 encapsulin shell protein
Ac: Type 1 encapsulin shell protein
Ad: Type 1 encapsulin shell protein
Ae: Type 1 encapsulin shell protein
Af: Type 1 encapsulin shell protein
Ag: Type 1 encapsulin shell protein
Ah: Type 1 encapsulin shell protein
Ai: Type 1 encapsulin shell protein
Aj: Type 1 encapsulin shell protein
Ak: Type 1 encapsulin shell protein
Al: Type 1 encapsulin shell protein
Am: Type 1 encapsulin shell protein
An: Type 1 encapsulin shell protein
Ao: Type 1 encapsulin shell protein
Ap: Type 1 encapsulin shell protein
Aq: Type 1 encapsulin shell protein
Ar: Type 1 encapsulin shell protein
As: Type 1 encapsulin shell protein
At: Type 1 encapsulin shell protein
Au: Type 1 encapsulin shell protein
Av: Type 1 encapsulin shell protein
Aw: Type 1 encapsulin shell protein
Ax: Type 1 encapsulin shell protein
Ay: Type 1 encapsulin shell protein


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


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

-
Components

#1: Protein ...
Type 1 encapsulin shell protein / Culture filtrate protein 29 / CFP29


Mass: 28863.346 Da / Num. of mol.: 60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Gene: enc, cfp29, Rv0798c / Production host: Escherichia coli (E. coli) / References: UniProt: I6WZG6

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Mycobacterium tuberculosis encapsulin / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 2 MDa / Experimental value: YES
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: 2400 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.75 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 251715 / Symmetry type: POINT

+
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://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