[English] 日本語
Yorodumi
- EMDB-17196: Structure of the protein cage composed of 12 identical 12-membere... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-17196
TitleStructure of the protein cage composed of 12 identical 12-membered protein rings
Map datamain map
Sample
  • Complex: Transcription attenuation protein MtrB
    • Protein or peptide: Transcription attenuation protein MtrB
Keywordsprotein cage / TRAP protein / VIRUS LIKE PARTICLE
Function / homologyTranscription attenuation protein MtrB / Tryptophan RNA-binding attenuator protein domain / Tryptophan RNA-binding attenuator protein / Tryptophan RNA-binding attenuator protein-like domain superfamily / DNA-templated transcription termination / regulation of DNA-templated transcription / RNA binding / Transcription attenuation protein MtrB
Function and homology information
Biological speciesHalalkalibacterium halodurans C-125 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsBiela AP
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2019/34/A/NZ1/00196 Poland
CitationJournal: J Mater Chem B / Year: 2024
Title: An artificial protein cage made from a 12-membered ring.
Authors: Izabela Stupka / Artur P Biela / Bernard Piette / Agnieszka Kowalczyk / Karolina Majsterkiewicz / Kinga Borzęcka-Solarz / Antonina Naskalska / Jonathan G Heddle /
Abstract: Artificial protein cages have great potential in diverse fields including as vaccines and drug delivery vehicles. TRAP-cage is an artificial protein cage notable for the way in which the interface ...Artificial protein cages have great potential in diverse fields including as vaccines and drug delivery vehicles. TRAP-cage is an artificial protein cage notable for the way in which the interface between its ring-shaped building blocks can be modified such that the conditions under which cages disassemble can be controlled. To date, TRAP-cages have been constructed from homo-11mer rings, , hendecamers. This is interesting as convex polyhedra with identical regular faces cannot be formed from hendecamers. TRAP-cage overcomes this limitation due to intrinsic flexibility, allowing slight deformation to absorb any error. The resulting TRAP-cage made from 24 TRAP 11mer rings is very close to regular with only very small errors necessary to allow the cage to form. The question arises as to the limits of the error that can be absorbed by a protein structure in this way before the formation of an apparently regular convex polyhedral becomes impossible. Here we use a naturally occurring TRAP variant consisting of twelve identical monomers (, a dodecamer) to probe these limits. We show that it is able to form an apparently regular protein cage consisting of twelve TRAP rings. Comparison of the cryo-EM structure of the new cage with theoretical models and related cages gives insight into the rules of cage formation and allows us to predict other cages that may be formed given TRAP-rings consisting of different numbers of monomers.
History
DepositionApr 24, 2023-
Header (metadata) releaseDec 27, 2023-
Map releaseDec 27, 2023-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_17196.png

Downloads & links

-
Map

FileDownload / File: emd_17196.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmain map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 270 pix.
= 287.55 Å		1.07 Å/pix.
x 270 pix.
= 287.55 Å		1.07 Å/pix.
x 270 pix.
= 287.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.531
Minimum - Maximum-0.3887152 - 1.142635
Average (Standard dev.)0.03176006 (±0.14840508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 287.55002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: hlaf map B

Fileemd_17196_half_map_1.map
Annotationhlaf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_17196_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Transcription attenuation protein MtrB

EntireName: Transcription attenuation protein MtrB
Components
  • Complex: Transcription attenuation protein MtrB
    • Protein or peptide: Transcription attenuation protein MtrB

-
Supramolecule #1: Transcription attenuation protein MtrB

SupramoleculeName: Transcription attenuation protein MtrB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: protein cage composed of 12 identical 12-membered TRAP rings
Source (natural)Organism: Halalkalibacterium halodurans C-125 (bacteria)
Molecular weightTheoretical: 1.2 MDa

-
Macromolecule #1: Transcription attenuation protein MtrB

MacromoleculeName: Transcription attenuation protein MtrB / type: protein_or_peptide / ID: 1 / Details: single point mutation at position 37 / Enantiomer: LEVO
Source (natural)Organism: Halalkalibacterium halodurans C-125 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MNVGDNSNFF VIKAKENGVN VFGMTRGTDT RFHHSECLDK GEVMIAQFTE HTSAVKIRGK AIIQTSYGTL DTEKDE

UniProtKB: Transcription attenuation protein MtrB

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 848602 / Details: auto picked particles
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: T (tetrahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 156357
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Avg.num./class: 150000 / Software - Name: cryoSPARC
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