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

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Basic information

Entry
Database: PDB / ID: 8rc6
TitleCryo-EM structure of hexameric BTB domain of Drosophila CG6765 protein
ComponentsBTB domain of CG6765 protein
KeywordsTRANSCRIPTION / DNA-binding / transcription regulation / oligomerization
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsBonchuk, A.N. / Naschberger, A. / Baradaran, R.
Funding support Russian Federation, 1items
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, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BTB domain of CG6765 protein
B: BTB domain of CG6765 protein
C: BTB domain of CG6765 protein
D: BTB domain of CG6765 protein
E: BTB domain of CG6765 protein
F: BTB domain of CG6765 protein


Theoretical massNumber of molelcules
Total (without water)87,2616
Polymers87,2616
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
BTB domain of CG6765 protein


Mass: 14543.481 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dmel\CG6765, CG6765, Dmel_CG6765 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9VSL1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: CELL / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Hexameric BTB domain of CG6765 protein / Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4 / Details: 20mM Tris, pH 7.4, 50mM NaCl, 1mM DTT
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 400 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.1 sec. / Electron dose: 40.3 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of real images: 9757

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10cryoSPARCinitial Euler assignment
11RELIONfinal Euler assignment
12RELIONclassification
13RELION53D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 480721
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 197562 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0056262
ELECTRON MICROSCOPYf_angle_d0.5538534
ELECTRON MICROSCOPYf_dihedral_angle_d12.3152238
ELECTRON MICROSCOPYf_chiral_restr0.042990
ELECTRON MICROSCOPYf_plane_restr0.0041078

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