[English] 日本語
Yorodumi
- EMDB-13924: Shape-morphing of an artificial protein cage with unusual geometr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13924
TitleShape-morphing of an artificial protein cage with unusual geometry induced by a single amino acid change
Map datamain map
Sample
  • Complex: artificail protein cage made out of 20 copies of TRAP ring
    • Protein or peptide: artificial protein cage made out of 20 TRAP protein rings
KeywordsTRAP / protein cage / complex / RNA BINDING PROTEIN
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 / identical protein binding / Transcription attenuation protein MtrB
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.13 Å
AuthorsBiela AP / Sharma M / Kowalczyk A / Borzecka-Solarz K / Piette BMAG / Bishop J / Kukura P / Benesch J / Imamura M / Scheuring S / Heddle JG
Funding support Poland, 2 items
OrganizationGrant numberCountry
Polish National Science Centre2016/20/W/NZ1/00095 Poland
Polish National Science Centre2019/34/A/NZ1/00196 Poland
CitationJournal: ACS Nanosci Au / Year: 2022
Title: Shape-Morphing of an Artificial Protein Cage with Unusual Geometry Induced by a Single Amino Acid Change.
Authors: Mohit Sharma / Artur P Biela / Agnieszka Kowalczyk / Kinga Borzęcka-Solarz / Bernard M A G Piette / Szymon Gaweł / Joshua Bishop / Philipp Kukura / Justin L P Benesch / Motonori Imamura / ...Authors: Mohit Sharma / Artur P Biela / Agnieszka Kowalczyk / Kinga Borzęcka-Solarz / Bernard M A G Piette / Szymon Gaweł / Joshua Bishop / Philipp Kukura / Justin L P Benesch / Motonori Imamura / Simon Scheuring / Jonathan G Heddle /
Abstract: Artificial protein cages are constructed from multiple protein subunits. The interaction between the subunits, notably the angle formed between them, controls the geometry of the resulting cage. ...Artificial protein cages are constructed from multiple protein subunits. The interaction between the subunits, notably the angle formed between them, controls the geometry of the resulting cage. Here, using the artificial protein cage, "TRAP-cage", we show that a simple alteration in the position of a single amino acid responsible for Au(I)-mediated subunit-subunit interactions in the constituent ring-shaped building blocks results in a more acute dihedral angle between them. In turn, this causes a dramatic shift in the structure from a 24-ring cage with an octahedral symmetry to a 20-ring cage with a C2 symmetry. This symmetry change is accompanied by a decrease in the number of Au(I)-mediated bonds between cysteines and a concomitant change in biophysical properties of the cage.
History
DepositionNov 30, 2021-
Header (metadata) releaseMay 11, 2022-
Map releaseMay 11, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13924.png

Downloads & links

-
Map

FileDownload / File: emd_13924.map.gz / Format: CCP4 / Size: 347.6 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.)
0.86 Å/pix.
x 450 pix.
= 387. Å		0.86 Å/pix.
x 450 pix.
= 387. Å		0.86 Å/pix.
x 450 pix.
= 387. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.077
Minimum - Maximum-0.15781957 - 0.25684986
Average (Standard dev.)0.00093048264 (±0.021951739)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions450450450
Spacing450450450
CellA=B=C: 387.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : artificail protein cage made out of 20 copies of TRAP ring

EntireName: artificail protein cage made out of 20 copies of TRAP ring
Components
  • Complex: artificail protein cage made out of 20 copies of TRAP ring
    • Protein or peptide: artificial protein cage made out of 20 TRAP protein rings

-
Supramolecule #1: artificail protein cage made out of 20 copies of TRAP ring

SupramoleculeName: artificail protein cage made out of 20 copies of TRAP ring
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Molecular weightTheoretical: 1.8 MDa

-
Macromolecule #1: artificial protein cage made out of 20 TRAP protein rings

MacromoleculeName: artificial protein cage made out of 20 TRAP protein rings
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Geobacillus stearothermophilus (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MYTNSDFVVI KALEDGVNVI GLTRGADTRF HHCEKLDKGE VLIAQFTEHT SAIKVRGKAY IQTSHGVIES EGKK

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 R1.2/1.3 / Material: MOLYBDENUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 70 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 1013 / Details: manually picked particles
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15.0) / Number images used: 113296
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 2.15.0)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC (ver. 2.15.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 2.15.0) / Details: class1 - 118,270 class2 - 17,672 class3 - 21,706
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://pdbjlvh1.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