[English] 日本語
Yorodumi
- EMDB-8747: Cryo-EM reconstruction of the HO microcompartment shell -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8747
TitleCryo-EM reconstruction of the HO microcompartment shell
Map dataCryo-EM reconstruction of the HO microcompartment shell
Sample
  • Complex: BMC (bacterial microcompartment) shell
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. ...Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / CcmK/CsoS1, bacterial microcompartment domain / Bacterial microcompartments protein, conserved site / Bacterial microcompartment (BMC) domain signature. / Bacterial microcompartment (BMC) domain profile. / BMC domain / Bacterial microcompartment domain / CcmK-like superfamily / BMC
Similarity search - Domain/homology
Bacterial microcompartment shell vertex protein / Bacterial microcompartment protein homohexamer / Bacterial microcompartment protein trimer-2
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsSutter M / Greber BJ / Aussignargues C / Kerfeld CA
CitationJournal: Science / Year: 2017
Title: Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell.
Authors: Markus Sutter / Basil Greber / Clement Aussignargues / Cheryl A Kerfeld /
Abstract: Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable ...Many bacteria contain primitive organelles composed entirely of protein. These bacterial microcompartments share a common architecture of an enzymatic core encapsulated in a selectively permeable protein shell; prominent examples include the carboxysome for CO fixation and catabolic microcompartments found in many pathogenic microbes. The shell sequesters enzymatic reactions from the cytosol, analogous to the lipid-based membrane of eukaryotic organelles. Despite available structural information for single building blocks, the principles of shell assembly have remained elusive. We present the crystal structure of an intact shell from , revealing the basic principles of bacterial microcompartment shell construction. Given the conservation among shell proteins of all bacterial microcompartments, these principles apply to functionally diverse organelles and can inform the design and engineering of shells with new functionalities.
History
DepositionMay 26, 2017-
Header (metadata) releaseJun 14, 2017-
Map releaseJul 5, 2017-
UpdateJun 13, 2018-
Current statusJun 13, 2018Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8747.png

Downloads & links

-
Map

FileDownload / File: emd_8747.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the HO microcompartment shell
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.8 Å/pix.
x 192 pix.
= 537.6 Å		2.8 Å/pix.
x 192 pix.
= 537.6 Å		2.8 Å/pix.
x 192 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.14585659 - 0.3632062
Average (Standard dev.)0.008368597 (±0.035658162)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.82.82.8
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1460.3630.008

-
Supplemental data

-
Sample components

-
Entire : BMC (bacterial microcompartment) shell

EntireName: BMC (bacterial microcompartment) shell
Components
  • Complex: BMC (bacterial microcompartment) shell

-
Supramolecule #1: BMC (bacterial microcompartment) shell

SupramoleculeName: BMC (bacterial microcompartment) shell / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Haliangium ochraceum (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 (DE3)
Molecular weightTheoretical: 6.5 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMTris-HClTris
50.0 mMSodium chlorideNaClSodium chloride
0.01 %NP-40 substitute
GridModel: Protochips CF-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Incubation on grid for 5-7 sec before plunging.

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated magnification: 107142 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 100000
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 15.0 µm / Number grids imaged: 1 / Number real images: 90 / Average exposure time: 0.4 sec. / Average electron dose: 25.0 e/Å2 / Details: Semi-automated collection using LEGINON
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 3750
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Details: CTF correction was performed inside RELION 1.4
Startup modelType of model: EMDB MAP
EMDB ID:

3351


Details: EMD-3351 was scaled to match the size of the BMC shell and low-pass filtered to avoid model bias.
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Details: Initial angle assignment during RELION 3D auto-refinement (maximum likelihood) based on initial reference. Icosahedral symmetry was imposed.
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 1.4)
Details: 3450 particle images were classified into 4 classes in RELION 1.4. Two classes (approx. 2600 particles) were included in the final refinement. Icosahedral symmetry was imposed during classification.
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Details: RELION 3D auto-refinement (maximum likelihood, gold standard). Icosahedral symmetry was imposed.
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 8.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Details: Icosahedral symmetry was imposed. / Number images used: 2600

-
Atomic model buiding 1

Initial model
PDB IDDetails

5v75

truncated to poly-Ala

5djb

truncated to poly-Ala

4jw0

truncated to poly-Ala
DetailsExisting high-resolution structures, truncated to poly-alanines, were docked into the map to create a model for molecular replacement phasing of BMC shell X-ray diffraction data.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

+
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