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- EMDB-14150: D. melanogaster 13-protofilament microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-14150
TitleD. melanogaster 13-protofilament microtubule
Map dataCryo-EM map of D. melanogaster microtubule
Sample
  • Complex: Microtubule
    • Protein or peptide: Tubulin alpha-1 chain
    • Protein or peptide: Tubulin beta-1 chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsCytyoskeleton / microtubules / cytomotive filaments / CELL CYCLE
Function / homology
Function and homology information


HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Neutrophil degranulation / astral microtubule / lysosome localization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton ...HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / Neutrophil degranulation / astral microtubule / lysosome localization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic cell cycle / microtubule / hydrolase activity / GTPase activity / centrosome / GTP binding / perinuclear region of cytoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / 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
Similarity search - Domain/homology
Tubulin alpha-1 chain / Tubulin beta-1 chain
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsWagstaff J / Planelles-Herrero VJ / Derivery E / Lowe J
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust202754/Z/16/Z United Kingdom
Medical Research Council (MRC, United Kingdom)U105184326 United Kingdom
CitationJournal: Sci Adv / Year: 2023
Title: Diverse cytomotive actins and tubulins share a polymerization switch mechanism conferring robust dynamics.
Authors: James Mark Wagstaff / Vicente José Planelles-Herrero / Grigory Sharov / Aisha Alnami / Frank Kozielski / Emmanuel Derivery / Jan Löwe /
Abstract: Protein filaments are used in myriads of ways to organize other molecules within cells. Some filament-forming proteins couple the hydrolysis of nucleotides to their polymerization cycle, thus ...Protein filaments are used in myriads of ways to organize other molecules within cells. Some filament-forming proteins couple the hydrolysis of nucleotides to their polymerization cycle, thus powering the movement of other molecules. These filaments are termed cytomotive. Only members of the actin and tubulin protein superfamilies are known to form cytomotive filaments. We examined the basis of cytomotivity via structural studies of the polymerization cycles of actin and tubulin homologs from across the tree of life. We analyzed published data and performed structural experiments designed to disentangle functional components of these complex filament systems. Our analysis demonstrates the existence of shared subunit polymerization switches among both cytomotive actins and tubulins, i.e., the conformation of subunits switches upon assembly into filaments. These cytomotive switches can explain filament robustness, by enabling the coupling of kinetic and structural polarities required for cytomotive behaviors and by ensuring that single cytomotive filaments do not fall apart.
History
DepositionJan 18, 2022-
Header (metadata) releaseNov 2, 2022-
Map releaseNov 2, 2022-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14150.png

Downloads & links

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Map

FileDownload / File: emd_14150.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of D. melanogaster microtubule
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
1.1 Å/pix.
x 392 pix.
= 431.984 Å		1.1 Å/pix.
x 392 pix.
= 431.984 Å		1.1 Å/pix.
x 392 pix.
= 431.984 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.102 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.582
Minimum - Maximum-3.03702 - 4.8064237
Average (Standard dev.)-0.00000000035555 (±0.23349538)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 431.984 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Microtubule

EntireName: Microtubule
Components
  • Complex: Microtubule
    • Protein or peptide: Tubulin alpha-1 chain
    • Protein or peptide: Tubulin beta-1 chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Microtubule

SupramoleculeName: Microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 1.170 MDa

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Macromolecule #1: Tubulin alpha-1 chain

MacromoleculeName: Tubulin alpha-1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 39 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 52.772324 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString: MHHHHHHEDQ VDPRLIDGKG GGGRPMRECI SIHVGQAGVQ IGNACWELYC LEHGIQPDGQ MPSDKTVGGG DDSFNTFFSE TGAGKHVPR AVFVDLEPTV VDEVRTGTYR QLFHPEQLIT GKEDAANNYA RGHYTIGKEI VDLVLDRIRK LADQCTGLQG F LIFHSFGG ...String:
MHHHHHHEDQ VDPRLIDGKG GGGRPMRECI SIHVGQAGVQ IGNACWELYC LEHGIQPDGQ MPSDKTVGGG DDSFNTFFSE TGAGKHVPR AVFVDLEPTV VDEVRTGTYR QLFHPEQLIT GKEDAANNYA RGHYTIGKEI VDLVLDRIRK LADQCTGLQG F LIFHSFGG GTGSGFTSLL MERLSVDYGK KSKLEFAIYP APQVSTAVVE PYNSILTTHT TLEHSDCAFM VDNEAIYDIC RR NLDIERP TYTNLNRLIG QIVSSITASL RFDGALNVDL TEFQTNLVPY PRIHFPLVTY APVISAEKAY HEQLSVAEIT NAC FEPANQ MVKCDPRHGK YMACCMLYRG DVVPKDVNAA IATIKTKRTI QFVDWCPTGF KVGINYQPPT VVPGGDLAKV QRAV CMLSN TTAIAEAWAR LDHKFDLMYA KRAFVHWYVG EGMEEGEFSE AREDLAALEK DYEEVGMDSG DGEGEGAEEY

UniProtKB: Tubulin alpha-1 chain

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Macromolecule #2: Tubulin beta-1 chain

MacromoleculeName: Tubulin beta-1 chain / type: protein_or_peptide / ID: 2 / Number of copies: 26 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 47.681707 KDa
SequenceString: REIVHIQAGQ CGNQIGAKFW EIISDEHGID ATGAYHGDSD LQLERINVYY NEASGGKYVP RAVLVDLEPG TMDSVRSGPF GQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKEAESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP D RIMNTYSV ...String:
REIVHIQAGQ CGNQIGAKFW EIISDEHGID ATGAYHGDSD LQLERINVYY NEASGGKYVP RAVLVDLEPG TMDSVRSGPF GQIFRPDNF VFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKEAESCDCL QGFQLTHSLG GGTGSGMGTL LISKIREEYP D RIMNTYSV VPSPKVSDTV VEPYNATLSV HQLVENTDET YCIDNEALYD ICFRTLKLTT PTYGDLNHLV SLTMSGVTTC LR FPGQLNA DLRKLAVNMV PFPRLHFFMP GFAPLTSRGS QQYRALTVPE LTQQMFDAKN MMAACDPRHG RYLTVAAIFR GRM SMKEVD EQMLNIQNKN SSYFVEWIPN NVKTAVCDIP PRGLKMSATF IGNSTAIQEL FKRISEQFTA MFRRKAFLHW YTGE GMDEM EFTEAESNMN DLVSEYQQYQ

UniProtKB: Tubulin beta-1 chain

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 39 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 39 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 26 / 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
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6.9
GridModel: Quantifoil R2/2 / Material: GOLD / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 32.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.5 CUT-OFF
Details: Resolution was determined against the atomic model, suing FSC 0.5
Number images used: 39594
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3j1t


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-7qup:
D. melanogaster 13-protofilament microtubule

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