[English] 日本語
Yorodumi
- EMDB-9310: Cryo-EM structure of the HO BMC shell: Icosahedral reconstruction... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9310
TitleCryo-EM structure of the HO BMC shell: Icosahedral reconstruction of the compacted subpopulation
Map dataCryo-EM of the HO shell, compacted class
Sample
  • Organelle or cellular component: Bacterial microcompartment shell from Haliangium ochraceum
    • Protein or peptide: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
    • Protein or peptide: Microcompartments protein
    • Protein or peptide: Microcompartments protein
Keywordsmicrocompartment / shell / compartmentalization / BMC fold / STRUCTURAL PROTEIN
Function / homology
Function and homology information


bacterial microcompartment
Similarity search - Function
Bacterial microcompartment (BMC) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / 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) circularly permuted domain / Bacterial microcompartment (BMC) circularly permuted domain profile. / 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
Bacterial microcompartment shell vertex protein / Bacterial microcompartment protein homohexamer / Bacterial microcompartment protein trimer-2
Similarity search - Component
Biological speciesHaliangium ochraceum (bacteria) / Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGreber BJ / Sutter M / Kerfeld CA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5 R01 AI114975-05 United States
Department of Energy (DOE, United States)DE-FG02-91ER20021 United States
CitationJournal: Structure / Year: 2019
Title: The Plasticity of Molecular Interactions Governs Bacterial Microcompartment Shell Assembly.
Authors: Basil J Greber / Markus Sutter / Cheryl A Kerfeld /
Abstract: Bacterial microcompartments (BMCs) are composed of an enzymatic core encapsulated by a selectively permeable protein shell that enhances catalytic efficiency. Many pathogenic bacteria derive ...Bacterial microcompartments (BMCs) are composed of an enzymatic core encapsulated by a selectively permeable protein shell that enhances catalytic efficiency. Many pathogenic bacteria derive competitive advantages from their BMC-based catabolism, implicating BMCs as drug targets. BMC shells are of interest for bioengineering due to their diverse and selective permeability properties and because they self-assemble. A complete understanding of shell composition and organization is a prerequisite for biotechnological applications. Here, we report the cryoelectron microscopy structure of a BMC shell at 3.0-Å resolution, using an image-processing strategy that allowed us to determine the previously uncharacterized structural details of the interactions formed by the BMC-T and BMC-T shell subunits in the context of the assembled shell. We found unexpected structural plasticity among these interactions, resulting in distinct shell populations assembled from varying numbers of the BMC-T and BMC-T subunits. We discuss the implications of these findings on shell assembly and function.
History
DepositionNov 6, 2018-
Header (metadata) releaseNov 21, 2018-
Map releaseMar 13, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing 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
  • Surface view with fitted model
  • Atomic models: PDB-6mzy
  • Surface level: 0.1
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6mzy
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9310.png

Downloads & links

-
Map

FileDownload / File: emd_9310.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM of the HO shell, compacted class
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 512 pix.
= 527.36 Å		1.03 Å/pix.
x 512 pix.
= 527.36 Å		1.03 Å/pix.
x 512 pix.
= 527.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1 / Movie #1: 0.1
Minimum - Maximum-0.2933102 - 0.5769061
Average (Standard dev.)0.0033968156 (±0.028628873)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 527.36 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z527.360527.360527.360
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.2930.5770.003

-
Supplemental data

-
Half map: unfiltered half map

Fileemd_9310_half_map_1.map
Annotationunfiltered half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: unfiltered half map

Fileemd_9310_half_map_2.map
Annotationunfiltered half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Bacterial microcompartment shell from Haliangium ochraceum

EntireName: Bacterial microcompartment shell from Haliangium ochraceum
Components
  • Organelle or cellular component: Bacterial microcompartment shell from Haliangium ochraceum
    • Protein or peptide: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
    • Protein or peptide: Microcompartments protein
    • Protein or peptide: Microcompartments protein

-
Supramolecule #1: Bacterial microcompartment shell from Haliangium ochraceum

SupramoleculeName: Bacterial microcompartment shell from Haliangium ochraceum
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Haliangium ochraceum (bacteria)
Molecular weightTheoretical: 6.5 MDa

-
Macromolecule #1: Ethanolamine utilization protein EutN/carboxysome structural prot...

MacromoleculeName: Ethanolamine utilization protein EutN/carboxysome structural protein Ccml
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Molecular weightTheoretical: 9.866319 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MVLGKVVGTV VASRKEPRIE GLSLLLVRAC DPDGTPTGGA VVCADAVGAG VGEVVLYASG SSARQTEVTN NRPVDATIMA IVDLVEMGG DVRFRKD

UniProtKB: Bacterial microcompartment shell vertex protein

-
Macromolecule #2: Microcompartments protein

MacromoleculeName: Microcompartments protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Molecular weightTheoretical: 10.126718 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MADALGMIEV RGFVGMVEAA DAMVKAAKVE LIGYEKTGGG YVTAVVRGDV AAVKAATEAG QRAAERVGEV VAVHVIPRPH VNVDAALPL GRTPGMDKSA

UniProtKB: Bacterial microcompartment protein homohexamer

-
Macromolecule #3: Microcompartments protein

MacromoleculeName: Microcompartments protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Molecular weightTheoretical: 22.904137 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSITLRTYIF LDALQPQLAT FIGKTARGFL PVPGQASLWV EIAPGIAINR VTDAALKATK VQPAVQVVER AYGLLEVHHF DQGEVLAAG STILDKLEVR EEGRLKPQVM THQIIRAVEA YQTQIINRNS QGMMILPGES LFILETQPAG YAVLAANEAE K AANVHLVN ...String:
MSITLRTYIF LDALQPQLAT FIGKTARGFL PVPGQASLWV EIAPGIAINR VTDAALKATK VQPAVQVVER AYGLLEVHHF DQGEVLAAG STILDKLEVR EEGRLKPQVM THQIIRAVEA YQTQIINRNS QGMMILPGES LFILETQPAG YAVLAANEAE K AANVHLVN VTPYGAFGRL YLAGSEAEID AAAEAAEAAI RSVSGVAQES FRDR

UniProtKB: Bacterial microcompartment protein trimer-2

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
50.0 mMSodium chlorideNaCl
0.01 %NP-40 substitute
GridSupport 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 / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: 5-7 sec incubation of the sample on the grid before blotting and plunging.

-
Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 928 / Average exposure time: 4.5 sec. / Average electron dose: 25.0 e/Å2
Details: 928 images retained after inspection for image quality. Movie frames were aligned and dose weighed using Motioncor2.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 3.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 48543 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: GATAN 626 SINGLE TILT LIQUID NITROGEN CRYO TRANSFER HOLDER
Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 31800
Details: 1000 particles were picked manually to generate reference templates for subsequent auto-picking in RELION 1.4.
Startup modelType of model: EMDB MAP
EMDB ID:

8747


Details: The reference was re-scaled and placed in a 512x512x512 pixel box to match the pixel size and appropriate box size for the data.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: FREALIGN (ver. 9)
Details: Frequency-limited refinement in FREALIGN. To avoid overfitting, resolutions higher than 3.6 Angstroms were excluded from the refinement. Icosahedral symmetry was imposed throughout the refinement procedure.
Number images used: 2276
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: FREALIGN (ver. 9)
Final 3D classificationNumber classes: 10 / Avg.num./class: 3180 / Software - Name: RELION (ver. 1.4)
Details: Icosahedral symmetry was applied during the classification.

-
Atomic model buiding 1

Initial modelPDB ID:

5v74


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6mzy:
Cryo-EM structure of the HO BMC shell: Icosahedral reconstruction of the compacted subpopulation

+
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