[English] 日本語
Yorodumi
- EMDB-30384: Simplified Alpha-Carboxysome, T=3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30384
TitleSimplified Alpha-Carboxysome, T=3
Map dataSimplified Alpha-Carboxysome, T=3
Sample
  • Organelle or cellular component: Simplified Alpha-Carboxysome, T=3
    • Protein or peptide: Unidentified carboxysome polypeptide
    • Protein or peptide: Major carboxysome shell protein 1A
KeywordsBacterial Microcompartment / Alpha-carboxysome / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


structural constituent of carboxysome shell / carboxysome / carbon fixation
Similarity search - Function
Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. ...Carboxysome shell vertex protein CsoS4A / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment vertex (BMV) domain profile. / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / CcmK/CsoS1, bacterial microcompartment domain / : / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / BMC / CcmK-like superfamily
Similarity search - Domain/homology
Carboxysome shell vertex protein CsoS4A / Major carboxysome shell protein CsoS1A
Similarity search - Component
Biological speciesHalothiobacillus neapolitanus (bacteria) / Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsTan YQ / Ali S
Funding support Singapore, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore) Singapore
CitationJournal: Biomacromolecules / Year: 2021
Title: Structure of a Minimal α-Carboxysome-Derived Shell and Its Utility in Enzyme Stabilization.
Authors: Yong Quan Tan / Samson Ali / Bo Xue / Wei Zhe Teo / Lay Hiang Ling / Maybelle Kho Go / Hong Lv / Robert C Robinson / Akihiro Narita / Wen Shan Yew /
Abstract: Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged ...Bacterial microcompartments are proteinaceous shells that encase specialized metabolic processes in bacteria. Recent advances in simplification of these intricate shells have encouraged bioengineering efforts. Here, we construct minimal shells derived from the α-carboxysome, which we term Cso-shell. Using cryogenic electron microscopy, the atomic-level structures of two shell forms were obtained, reinforcing notions of evolutionarily conserved features in bacterial microcompartment shell architecture. Encapsulation peptide sequences that facilitate loading of heterologous protein cargo within the shells were identified. We further provide a first demonstration in utilizing minimal bacterial microcompartment-derived shells for hosting heterologous enzymes. Cso-shells were found to stabilize enzymatic activities against heat shock, presence of methanol co-solvent, consecutive freeze-thawing, and alkaline environments. This study yields insights into α-carboxysome assembly and advances the utility of synthetic bacterial microcompartments as nanoreactors capable of stabilizing enzymes with varied properties and reaction chemistries.
History
DepositionJul 16, 2020-
Header (metadata) releaseAug 25, 2021-
Map releaseAug 25, 2021-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ckb
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ckb
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30384.png

Downloads & links

-
Map

FileDownload / File: emd_30384.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSimplified Alpha-Carboxysome, T=3
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å		0.86 Å/pix.
x 320 pix.
= 275.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.0645458 - 0.121782154
Average (Standard dev.)0.0018871978 (±0.009681336)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 275.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z275.200275.200275.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ384384384
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0650.1220.002

-
Supplemental data

-
Sample components

-
Entire : Simplified Alpha-Carboxysome, T=3

EntireName: Simplified Alpha-Carboxysome, T=3
Components
  • Organelle or cellular component: Simplified Alpha-Carboxysome, T=3
    • Protein or peptide: Unidentified carboxysome polypeptide
    • Protein or peptide: Major carboxysome shell protein 1A

-
Supramolecule #1: Simplified Alpha-Carboxysome, T=3

SupramoleculeName: Simplified Alpha-Carboxysome, T=3 / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 1.7 MDa

-
Macromolecule #1: Unidentified carboxysome polypeptide

MacromoleculeName: Unidentified carboxysome polypeptide / type: protein_or_peptide / ID: 1 / Number of copies: 60 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
Molecular weightTheoretical: 10.17364 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MKIMQVEKTL VSTNRIADMG HKPLLVVWEK PGAPRQVAVD AIGCIPGDWV LCVGSSAARE AAGSKSYPSD LTIIGIIDQW NGEGSSWSH PQFEK

UniProtKB: Carboxysome shell vertex protein CsoS4A

-
Macromolecule #2: Major carboxysome shell protein 1A

MacromoleculeName: Major carboxysome shell protein 1A / type: protein_or_peptide / ID: 2 / Number of copies: 120 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (strain ATCC 23641 / c2) (bacteria)
Strain: ATCC 23641 / c2
Molecular weightTheoretical: 9.973478 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADVTGIALG MIETRGLVPA IEAADAMTKA AEVRLVGRQF VGGGYVTVLV RGETGAVNAA VRAGADACER VGDGLVAAHI IARVHSEVE NILPKAPQA

UniProtKB: Major carboxysome shell protein CsoS1A

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: LEICA EM GP / Details: Blot for 1.0 - 2.5 seconds.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 64.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 94129
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.7) / Software - details: RELION was used throughout / Number images used: 11468
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final 3D classificationSoftware - Name: RELION (ver. 3.0.7)
Software - details: Particles were selected from 2D classification in RELION

-
Atomic model buiding 1

Initial model
PDB IDChain

2rcf

source_name: PDB, initial_model_type: experimental model

2ewh

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7ckb:
Simplified Alpha-Carboxysome, T=3

+
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