[English] 日本語
- PDB-6n0g: Cryo-EM structure of the HO BMC shell: subregion classified for B... -

Open data

ID or keywords:


Basic information

Database: PDB / ID: 6n0g
TitleCryo-EM structure of the HO BMC shell: subregion classified for BMC-T: TS-TDTDTD
Components(Microcompartments proteinBacterial microcompartment) x 3
KeywordsSTRUCTURAL PROTEIN / microcompartment / shell / compartmentalization / BMC fold
Function / homologyMicrocompartment protein, bacteria / Polyhedral organelle shell protein PduT / Bacterial microcompartments protein, conserved site / CcmK-like superfamily / BMC domain / Microcompartments protein / Microcompartments protein / Microcompartments protein
Function and homology information
Biological speciesHaliangium ochraceum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGreber, B.J. / Sutter, M. / Kerfeld, C.A.
Funding support United States, 2items
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.
Validation Report
SummaryFull reportAbout validation report
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure visualization

  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-9315
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:

Downloads & links


Deposited unit
A: Microcompartments protein
B: Microcompartments protein
C: Microcompartments protein
GA: Microcompartments protein
GB: Microcompartments protein
GC: Microcompartments protein
GD: Microcompartments protein
GE: Microcompartments protein
GF: Microcompartments protein
HA: Microcompartments protein
HB: Microcompartments protein
HC: Microcompartments protein
HD: Microcompartments protein
HE: Microcompartments protein
HF: Microcompartments protein
IA: Microcompartments protein
IB: Microcompartments protein
IC: Microcompartments protein
ID: Microcompartments protein
IE: Microcompartments protein
IF: Microcompartments protein
JA: Microcompartments protein
JB: Microcompartments protein
JC: Microcompartments protein
JD: Microcompartments protein
JE: Microcompartments protein
JF: Microcompartments protein
KA: Microcompartments protein
KB: Microcompartments protein
KC: Microcompartments protein
KD: Microcompartments protein
KE: Microcompartments protein
KF: Microcompartments protein
LA: Microcompartments protein
LB: Microcompartments protein
LC: Microcompartments protein
LD: Microcompartments protein
LE: Microcompartments protein
LF: Microcompartments protein
G: Microcompartments protein
H: Microcompartments protein
I: Microcompartments protein
J: Microcompartments protein
K: Microcompartments protein
L: Microcompartments protein
M: Microcompartments protein
N: Microcompartments protein
O: Microcompartments protein
P: Microcompartments protein
Q: Microcompartments protein
R: Microcompartments protein
S: Microcompartments protein
T: Microcompartments protein
U: Microcompartments protein
V: Microcompartments protein
W: Microcompartments protein
X: Microcompartments protein

Theoretical massNumber of molelcules
Total (without water)842,60657

  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area155090 Å2
ΔGint-939 kcal/mol
Surface area240450 Å2


#1: Protein Microcompartments protein / Bacterial microcompartment / HO-5812

Mass: 21923.199 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_5812 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LHE3
#2: Protein ...
Microcompartments protein / Bacterial microcompartment / HO-5815

Mass: 10126.718 Da / Num. of mol.: 36
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_5815 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LID5
#3: Protein
Microcompartments protein / Bacterial microcompartment / HO-5816

Mass: 22904.137 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2 / Gene: Hoch_5816 / Production host: Escherichia coli (E. coli) / References: UniProt: D0LID6

Experimental details


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

Sample preparation

ComponentName: Bacterial microcompartment shell from Haliangium ochraceum
Molecular weightValue: 6.5 MDa / Experimental value: NO
Source (natural)Organism: Haliangium ochraceum (strain DSM 14365 / JCM 11303 / SMP-2) (bacteria)
Strain: DSM 14365 / JCM 11303 / SMP-2
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
Buffer component
120 mMTris-HClTris1
250 mMsodium chlorideNaClSodium chloride1
30.01 %NP-40 substitute1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: 5-7 second incubation of the sample on the grid before blotting and plunging

Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 48543 X / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 4.5 sec. / Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 928
Details: 928 images retained after inspection for image quality.
Image scansSampling size: 5 µm / Width: 3838 / Height: 3710 / Movie frames/image: 30 / Used frames/image: 1-30


EM software
2Leginonimage acquisition
4CTFFIND4CTF correction
7Cootmodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
12RELION1.43D reconstruction
13PHENIXmodel refinement
CTF correctionDetails: Initial CTF fitting using CTFFIND4, CTF correction applied within RELION
Particle selectionNum. of particles selected: 31800
Details: 1000 particles were picked manually to generate reference templates for subsequent auto-picking in RELION 1.4.
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80783 / Algorithm: FOURIER SPACE
Details: The selected particle subset was refined without masking and subsequently masked to reveal only the subregion of the BMC shell to which the focused classification had been applied.
Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Atomic model building
IDPDB-ID3D fitting-ID

About Yorodumi


Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

Read more


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.

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