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- EMDB-3726: BtubABC mini microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-3726
TitleBtubABC mini microtubule
Map dataBtubABC mini microtubule
Sample
  • Complex: BtubABC mini microtubule
    • Complex: BtubABC mini microtubule
      • Protein or peptide: Tubulin
      • Protein or peptide: Tubulin BtubB
    • Complex: BtubABC mini microtubule
      • Protein or peptide: Bacterial kinesin light chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information


microtubule-based process / structural constituent of cytoskeleton / microtubule / hydrolase activity / GTPase activity / protein serine/threonine kinase activity / GTP binding
Similarity search - Function
MalT-like TPR region / MalT-like TPR region / Tetratricopeptide repeat / Tetratricopeptide repeat / Alpha tubulin / Beta tubulin / TPR repeat profile. / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain ...MalT-like TPR region / 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
Bacterial kinesin light chain / Tubulin BtubB / Tubulin
Similarity search - Component
Biological speciesProsthecobacter dejongeii (bacteria) / Prosthecobacter vanneervenii (bacteria)
Methodhelical reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsDeng X / Bharat TAM / 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, 2017-
Header (metadata) releaseJun 21, 2017-
Map releaseJul 19, 2017-
UpdateOct 3, 2018-
Current statusOct 3, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0967
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0967
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5o09
  • Surface level: 0.0967
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5o09
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3726.png

Downloads & links

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Map

FileDownload / File: emd_3726.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBtubABC mini microtubule
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 0.0967 / Movie #1: 0.0967
Minimum - Maximum-0.42958683 - 0.73041767
Average (Standard dev.)0.00006278253 (±0.03188777)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 375.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z375.200375.200375.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.4300.7300.000

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Supplemental data

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Sample components

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Entire : BtubABC mini microtubule

EntireName: BtubABC mini microtubule
Components
  • Complex: BtubABC mini microtubule
    • Complex: BtubABC mini microtubule
      • Protein or peptide: Tubulin
      • Protein or peptide: Tubulin BtubB
    • Complex: BtubABC mini microtubule
      • Protein or peptide: Bacterial kinesin light chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: BtubABC mini microtubule

SupramoleculeName: BtubABC mini microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: BtubABC mini microtubule

SupramoleculeName: BtubABC mini microtubule / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Prosthecobacter dejongeii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: BtubABC mini microtubule

SupramoleculeName: BtubABC mini microtubule / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Prosthecobacter vanneervenii (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Tubulin

MacromoleculeName: Tubulin / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Prosthecobacter dejongeii (bacteria)
Molecular weightTheoretical: 47.071582 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VNNTIVVSIG QAGNQIAASF WKTVCLEHGI DPLTGQTAPG VAPRGNWSSF FSKLGESSSG SYVPRAIMVD LEPSVIDNVK ATSGSLFNP ANLISRTEGA GGNFAVGYLG AGREVLPEVM SRLDYEIDKC DNVGGIIVLH AIGGGTGSGF GALLIESLKE K YGEIPVLS ...String:
VNNTIVVSIG QAGNQIAASF WKTVCLEHGI DPLTGQTAPG VAPRGNWSSF FSKLGESSSG SYVPRAIMVD LEPSVIDNVK ATSGSLFNP ANLISRTEGA GGNFAVGYLG AGREVLPEVM SRLDYEIDKC DNVGGIIVLH AIGGGTGSGF GALLIESLKE K YGEIPVLS CAVLPSPQVS SVVTEPYNTV FALNTLRRSA DACLIFDNEA LFDLAHRKWN IESPTVDDLN LLITEALAGI TA SMRFSGF LTVEITLREL LTNLVPQPSL HFLMCAFAPL TPPDRSKFEE LGIEEMIKSL FDNGSVFAAC SPMEGRFLST AVL YRGIME DKPLADAALA AMREKLPLTY WIPTAFKIGY VEQPGISHRK SMVLLANNTE IARVLDRICH NFDKLWQRKA FANW YLNEG MSEEQINVLR ASAQELVQSY QVAEESGA

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Macromolecule #2: Tubulin BtubB

MacromoleculeName: Tubulin BtubB / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Prosthecobacter dejongeii (bacteria)
Molecular weightTheoretical: 46.465508 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VREILSIHVG QCGNQIADSF WRLALREHGL TEAGTLKEGS NAAANSNMEV FFHKVRDGKY VPRAVLVDLE PGVIARIEGG DMSQLFDES SIVRKIPGAA NNWARGYNVE GEKVIDQIMN VIDSAVEKTK GLQGFLMTHS IGGGSGSGLG SLILERLRQA Y PKKRIFTF ...String:
VREILSIHVG QCGNQIADSF WRLALREHGL TEAGTLKEGS NAAANSNMEV FFHKVRDGKY VPRAVLVDLE PGVIARIEGG DMSQLFDES SIVRKIPGAA NNWARGYNVE GEKVIDQIMN VIDSAVEKTK GLQGFLMTHS IGGGSGSGLG SLILERLRQA Y PKKRIFTF SVVPSPLISD SAVEPYNAIL TLQRILDNAD GAVLLDNEAL FRIAKAKLNR SPNYMDLNNI IALIVSSVTA SL RFPGKLN TDLSEFVTNL VPFPGNHFLT ASFAPMRGAG QEGQVRTNFP DLARETFAQD NFTAAIDWQQ GVYLAASALF RGD VKAKDV DENMATIRKS LNYASYMPAS GGLKLGYAET APEGFASSGL ALVNHTGIAA VFERLIAQFD IMFDNHAYTH WYEN AGVSR DMMAKARNQI ATLAQSYRDA S

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Macromolecule #3: Bacterial kinesin light chain

MacromoleculeName: Bacterial kinesin light chain / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Prosthecobacter vanneervenii (bacteria)
Molecular weightTheoretical: 27.135703 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: DTALERQIAS ASRSVEEARR LAYHDPIRVG ALVEQISVLA DLRQKEGDFR KAESLYREAL FRAQELRKQD PDLLTGIYSL LAHLYDRWG RMDKAAEFYE LALKISAENG LEESDKVATI KNNLAMIFKQ LRKFERAEGY YCEALETFQR LDGEQSARVA S VYNNLGVL ...String:
DTALERQIAS ASRSVEEARR LAYHDPIRVG ALVEQISVLA DLRQKEGDFR KAESLYREAL FRAQELRKQD PDLLTGIYSL LAHLYDRWG RMDKAAEFYE LALKISAENG LEESDKVATI KNNLAMIFKQ LRKFERAEGY YCEALETFQR LDGEQSARVA S VYNNLGVL YYSHMDVDRA QVMHERALAI RQNLHEGQMD PADLSQTFIN LGAVYKAAGD FQKAEACVDR AKRIRAAMNG

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Macromolecule #4: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 16 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM / Guanosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.7
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number real images: 6105 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Details: Subtomogram averaged cryotomography map (reference free alignment, no symmetry imposed)
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 79.31 Å
Applied symmetry - Helical parameters - Δ&Phi: -5.54 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 257661
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL / Protocol: OTHER / Target criteria: R-factor
Output model

PDB-5o09:
BtubABC mini microtubule

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