[English] 日本語
Yorodumi
- EMDB-14589: Subtomogram averaging structure of tandem Rubiscos from H. neapol... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-14589
TitleSubtomogram averaging structure of tandem Rubiscos from H. neapolitanus carboxysomes
Map datamerged map
Sample
  • Complex: alpha carboxysomes
    • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), large subunit
    • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), small subunit
Biological speciesHalothiobacillus neapolitanus (bacteria)
Methodsubtomogram averaging / cryo EM / Resolution: 3.3 Å
AuthorsNi T / Zhu Y / Zhang P
Funding supportEuropean Union, United Kingdom, 3 items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
Wellcome Trust United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
Citation
Journal: Nat Commun / Year: 2022
Title: Structure and assembly of cargo Rubisco in two native α-carboxysomes.
Authors: Tao Ni / Yaqi Sun / Will Burn / Monsour M J Al-Hazeem / Yanan Zhu / Xiulian Yu / Lu-Ning Liu / Peijun Zhang /
Abstract: Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase ...Carboxysomes are a family of bacterial microcompartments in cyanobacteria and chemoautotrophs. They encapsulate Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) and carbonic anhydrase catalyzing carbon fixation inside a proteinaceous shell. How Rubisco complexes pack within the carboxysomes is unknown. Using cryo-electron tomography, we determine the distinct 3D organization of Rubisco inside two distant α-carboxysomes from a marine α-cyanobacterium Cyanobium sp. PCC 7001 where Rubiscos are organized in three concentric layers, and from a chemoautotrophic bacterium Halothiobacillus neapolitanus where they form intertwining spirals. We further resolve the structures of native Rubisco as well as its higher-order assembly at near-atomic resolutions by subtomogram averaging. The structures surprisingly reveal that the authentic intrinsically disordered linker protein CsoS2 interacts with Rubiscos in native carboxysomes but functions distinctively in the two α-carboxysomes. In contrast to the uniform Rubisco-CsoS2 association in the Cyanobium α-carboxysome, CsoS2 binds only to the Rubiscos close to the shell in the Halo α-carboxysome. Our findings provide critical knowledge of the assembly principles of α-carboxysomes, which may aid in the rational design and repurposing of carboxysome structures for new functions.
#1: Journal: bioRxiv / Year: 2022
Title: Tales of Two alpha Carboxysomes the Structure and Assembly of Cargo Rubisco
Authors: Ni T / Sun Y / Seaton-Burn W / AI-Hazeem M / Zhu Y / Yu X / Liu L / Zhang P
History
DepositionMar 24, 2022-
Header (metadata) releaseJul 13, 2022-
Map releaseJul 13, 2022-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_14589.png

Downloads & links

-
Map

FileDownload / File: emd_14589.map.gz / Format: CCP4 / Size: 85.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmerged map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 282 pix.
= 377.88 Å		1.34 Å/pix.
x 282 pix.
= 377.88 Å		1.34 Å/pix.
x 282 pix.
= 377.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5
Minimum - Maximum-10.125993 - 13.451159
Average (Standard dev.)0.016725548 (±0.48746094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions282282282
Spacing282282282
CellA=B=C: 377.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half1 map

Fileemd_14589_half_map_1.map
Annotationhalf1 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half2 map

Fileemd_14589_half_map_2.map
Annotationhalf2 map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : alpha carboxysomes

EntireName: alpha carboxysomes
Components
  • Complex: alpha carboxysomes
    • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), large subunit
    • Protein or peptide: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), small subunit

-
Supramolecule #1: alpha carboxysomes

SupramoleculeName: alpha carboxysomes / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)

-
Macromolecule #1: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), large ...

MacromoleculeName: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), large subunit
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
SequenceString: MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV AAESSTGTWT TVWTDLLTD MDYYKGRAYR IEDVPGDDAA FYAFIAYPID LFEEGSVVNV FTSLVGNVFG F KAVRGLRL EDVRFPLAYV KTCGGPPHGI QVERDKMNKY GRPLLGCTIK ...String:
MAVKKYSAGV KEYRQTYWMP EYTPLDSDIL ACFKITPQPG VDREEAAAAV AAESSTGTWT TVWTDLLTD MDYYKGRAYR IEDVPGDDAA FYAFIAYPID LFEEGSVVNV FTSLVGNVFG F KAVRGLRL EDVRFPLAYV KTCGGPPHGI QVERDKMNKY GRPLLGCTIK PKLGLSAKNY GR AVYECLR GGLDFTKDDE NINSQPFMRW RDRFLFVQDA TETAEAQTGE RKGHYLNVTA PTP EEMYKR AEFAKEIGAP IIMHDYITGG FTANTGLAKW CQDNGVLLHI HRAMHAVIDR NPNH GIHFR VLTKILRLSG GDHLHTGTVV GKLEGDRAST LGWIDLLRES FIPEDRSRGI FFDQD WGSM PGVFAVASGG IHVWHMPALV NIFGDDSVLQ FGGGTLGHPW GNAAGAAANR VALEAC VEA RNQGRDIEKE GKEILTAAAQ HSPELKIAME TWKEIKFEFD TVDKLDTQNR

-
Macromolecule #2: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), small ...

MacromoleculeName: Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), small subunit
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Halothiobacillus neapolitanus (bacteria)
SequenceString:
MAEMQDYKQS LKYETFSYLP PMNAERIRAQ IKYAIAQGWS PGIEHVEVKN SMNQYWYMWK LPFFGEQNV DNVLAEIEAC RSAYPTHQVK LVAYDNYAQS LGLAFVVYRG N

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 3.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 60 / Number images used: 149479
Final 3D classificationNumber classes: 1
Final angle assignmentType: OTHER / Software - Name: emClarity / Details: cross correlation
Final reconstructionApplied symmetry - Point group: D4 (2x4 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: emClarity / Number subtomograms used: 149479
Detailsthe raw micrographs were motioncorrected and stacked into tilt-series, aligned in etomo, the processed in emClarity
FSC plot (resolution estimation)

+
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