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- EMDB-19049: Cryo-EM structure of hexameric BTB domain of Drosophila CG6765 protein -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-19049
TitleCryo-EM structure of hexameric BTB domain of Drosophila CG6765 protein
Map dataMain map with RELION Blush regularisation applied
Sample
  • Cell: Hexameric BTB domain of CG6765 protein
    • Protein or peptide: BTB domain of CG6765 protein
KeywordsDNA-binding / transcription regulation / oligomerization / TRANSCRIPTION
Function / homology
Function and homology information


developmental process involved in reproduction / animal organ development / neuron development / regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
: / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type
Similarity search - Domain/homology
Uncharacterized protein, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBonchuk AN / Naschberger A / Baradaran R
Funding support Russian Federation, 1 items
OrganizationGrant numberCountry
Russian Science Foundation19-74-10099 Russian Federation
CitationJournal: Elife / Year: 2024
Title: The Arthropoda-specific Tramtrack group BTB protein domains use previously unknown interface to form hexamers.
Authors: Artem N Bonchuk / Konstantin I Balagurov / Rozbeh Baradaran / Konstantin M Boyko / Nikolai N Sluchanko / Anastasia M Khrustaleva / Anna D Burtseva / Olga V Arkova / Karina K Khalisova / ...Authors: Artem N Bonchuk / Konstantin I Balagurov / Rozbeh Baradaran / Konstantin M Boyko / Nikolai N Sluchanko / Anastasia M Khrustaleva / Anna D Burtseva / Olga V Arkova / Karina K Khalisova / Vladimir O Popov / Andreas Naschberger / Pavel G Georgiev /
Abstract: BTB (bric-a-brack, Tramtrack, and broad complex) is a diverse group of protein-protein interaction domains found within metazoan proteins. Transcription factors contain a dimerizing BTB subtype with ...BTB (bric-a-brack, Tramtrack, and broad complex) is a diverse group of protein-protein interaction domains found within metazoan proteins. Transcription factors contain a dimerizing BTB subtype with a characteristic N-terminal extension. The Tramtrack group (TTK) is a distinct type of BTB domain, which can multimerize. Single-particle cryo-EM microscopy revealed that the TTK-type BTB domains assemble into a hexameric structure consisting of three canonical BTB dimers connected through a previously uncharacterized interface. We demonstrated that the TTK-type BTB domains are found only in Arthropods and have undergone lineage-specific expansion in modern insects. The genome encodes 24 transcription factors with TTK-type BTB domains, whereas only four have non-TTK-type BTB domains. Yeast two-hybrid analysis revealed that the TTK-type BTB domains have an unusually broad potential for heteromeric associations presumably through a dimer-dimer interaction interface. Thus, the TTK-type BTB domains are a structurally and functionally distinct group of protein domains specific to Arthropodan transcription factors.
History
DepositionDec 6, 2023-
Header (metadata) releaseSep 11, 2024-
Map releaseSep 11, 2024-
UpdateSep 11, 2024-
Current statusSep 11, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19049.png

Downloads & links

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Map

FileDownload / File: emd_19049.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map with RELION Blush regularisation applied
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 448 pix.
= 326.592 Å		0.73 Å/pix.
x 448 pix.
= 326.592 Å		0.73 Å/pix.
x 448 pix.
= 326.592 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00349
Minimum - Maximum-0.0074587828 - 0.016640231
Average (Standard dev.)0.000007679063 (±0.00022136905)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 326.59198 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19049_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Hexameric BTB domain of CG6765 protein

EntireName: Hexameric BTB domain of CG6765 protein
Components
  • Cell: Hexameric BTB domain of CG6765 protein
    • Protein or peptide: BTB domain of CG6765 protein

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Supramolecule #1: Hexameric BTB domain of CG6765 protein

SupramoleculeName: Hexameric BTB domain of CG6765 protein / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: BTB domain of CG6765 protein

MacromoleculeName: BTB domain of CG6765 protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 14.543481 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AENYHLKWDS HLTYLNSSIA TLYKNEKFAD VVLYSSYNSS GIPSDIPTVG ISAHKFILSA SSQFFATMFE TAPITNPNGV LYVVLPPDL SHRAIQILVQ YMYSGEATVS NDILNEVLRG GEILKIRGLC RT

UniProtKB: Uncharacterized protein, isoform A

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statecell

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.4 / Details: 20mM Tris, pH 7.4, 50mM NaCl, 1mM DTT
GridMaterial: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number real images: 9757 / Average exposure time: 4.1 sec. / Average electron dose: 40.3 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 480721
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 197562
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Avg.num./class: 190 / Software - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8rc6:
Cryo-EM structure of hexameric BTB domain of Drosophila CG6765 protein

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