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- PDB-5o09: BtubABC mini microtubule -

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Basic information

Entry
Database: PDB / ID: 5o09
TitleBtubABC mini microtubule
Components
  • Bacterial kinesin light chain
  • Tubulin
  • Tubulin BtubB
KeywordsSTRUCTURAL PROTEIN / bacterial cytoskeleton / microtubules
Function / homology
Function and homology information


microtubule-based process / structural constituent of cytoskeleton / microtubule / hydrolase activity / protein serine/threonine kinase activity / GTPase activity / GTP binding
Similarity search - Function
MalT-like TPR region / Tetratricopeptide repeat / Tetratricopeptide repeat / Alpha tubulin / Beta tubulin / TPR repeat profile. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site ...MalT-like TPR region / Tetratricopeptide repeat / Tetratricopeptide repeat / Alpha tubulin / Beta tubulin / TPR repeat profile. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tetratricopeptide repeats / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Bacterial kinesin light chain / Tubulin BtubB / Tubulin
Similarity search - Component
Biological speciesProsthecobacter dejongeii (bacteria)
Prosthecobacter vanneervenii (bacteria)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDeng, X. / Bharat, T.A.M. / Lowe, J.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Four-stranded mini microtubules formed by BtubAB show dynamic instability.
Authors: Xian Deng / Gero Fink / Tanmay A M Bharat / Shaoda He / Danguole Kureisaite-Ciziene / Jan Löwe /
Abstract: Microtubules, the dynamic, yet stiff hollow tubes built from αβ-tubulin protein heterodimers, are thought to be present only in eukaryotic cells. Here, we report a 3.6-Å helical reconstruction ...Microtubules, the dynamic, yet stiff hollow tubes built from αβ-tubulin protein heterodimers, are thought to be present only in eukaryotic cells. Here, we report a 3.6-Å helical reconstruction electron cryomicroscopy structure of four-stranded mini microtubules formed by bacterial tubulin-like BtubAB proteins. Despite their much smaller diameter, mini microtubules share many key structural features with eukaryotic microtubules, such as an M-loop, alternating subunits, and a seam that breaks overall helical symmetry. Using in vitro total internal reflection fluorescence microscopy, we show that bacterial mini microtubules treadmill and display dynamic instability, another hallmark of eukaryotic microtubules. The third protein in the gene cluster, BtubC, previously known as "bacterial kinesin light chain," binds along protofilaments every 8 nm, inhibits BtubAB mini microtubule catastrophe, and increases rescue. Our work reveals that some bacteria contain regulated and dynamic cytomotive microtubule systems that were once thought to be only useful in much larger and sophisticated eukaryotic cells.
History
DepositionMay 16, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Aug 30, 2017Group: Refinement description / Category: em_3d_fitting / Item: _em_3d_fitting.target_criteria
Revision 1.3Oct 4, 2017Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.pdb_format_compatible
Revision 1.4Oct 3, 2018Group: Advisory / Data collection / Derived calculations / Category: pdbx_validate_close_contact / struct_conn
Revision 1.5May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure viewerMolecule:
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Assembly

Deposited unit
1A: Tubulin
1B: Tubulin BtubB
1C: Bacterial kinesin light chain
2A: Tubulin
2B: Tubulin BtubB
2C: Bacterial kinesin light chain
3A: Tubulin
3B: Tubulin BtubB
3C: Bacterial kinesin light chain
4A: Tubulin
4B: Tubulin BtubB
4C: Bacterial kinesin light chain
5A: Tubulin
5B: Tubulin BtubB
5C: Bacterial kinesin light chain
6A: Tubulin
6B: Tubulin BtubB
6C: Bacterial kinesin light chain
7A: Tubulin
7B: Tubulin BtubB
7C: Bacterial kinesin light chain
8A: Tubulin
8B: Tubulin BtubB
8C: Bacterial kinesin light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)972,47440
Polymers965,38224
Non-polymers7,09116
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA

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Components

#1: Protein
Tubulin / Tubulin BtubA


Mass: 47071.582 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prosthecobacter dejongeii (bacteria) / Gene: btubA / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GCC5
#2: Protein
Tubulin BtubB


Mass: 46465.508 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prosthecobacter dejongeii (bacteria) / Gene: btubB / Production host: Escherichia coli (E. coli) / References: UniProt: Q8GCC1
#3: Protein
Bacterial kinesin light chain


Mass: 27135.703 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Prosthecobacter vanneervenii (bacteria)
Gene: bklc / Production host: Escherichia coli (E. coli) / References: UniProt: A8Y5U5
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1BtubABC mini microtubuleCOMPLEX#1-#30MULTIPLE SOURCES
2BtubABC mini microtubuleCOMPLEX#1-#21RECOMBINANT
3BtubABC mini microtubuleCOMPLEX#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Prosthecobacter dejongeii (bacteria)48465
33Prosthecobacter vanneervenii (bacteria)48466
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Image recordingElectron dose: 40 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k) / Num. of real images: 6105

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -5.54 ° / Axial rise/subunit: 79.31 Å / Axial symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 257661 / Symmetry type: HELICAL
Atomic model buildingProtocol: OTHER / Space: RECIPROCAL / Target criteria: R-factor

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