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- EMDB-14147: D. melanogaster alpha/beta tubulin heterodimer in the GDP form -

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Basic information

Entry
Database: EMDB / ID: EMD-14147
TitleD. melanogaster alpha/beta tubulin heterodimer in the GDP form
Map dataalpha/beta tubulin heterodimer from D. melanogaster in the GDP state.
Sample
  • Complex: alpha1/beta tubulin heterodimer
    • Complex: Tubulin alpha-1 chain
      • Protein or peptide: Tubulin alpha-1 chain
    • Complex: Tubulin beta-1 chain
      • Protein or peptide: Tubulin beta-1 chain
  • Ligand: GUANOSINE-5'-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 / astral microtubule / Neutrophil degranulation / lysosome localization / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...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 / astral microtubule / Neutrophil degranulation / lysosome localization / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / centrosome / GTP binding / perinuclear region of cytoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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: 3.2 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 17, 2022-
Header (metadata) releaseSep 21, 2022-
Map releaseSep 21, 2022-
UpdateOct 4, 2023-
Current statusOct 4, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14147.png

Downloads & links

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Map

FileDownload / File: emd_14147.map.gz / Format: CCP4 / Size: 98.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationalpha/beta tubulin heterodimer from D. melanogaster in the GDP state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.62 Å/pix.
x 296 pix.
= 184.112 Å		0.62 Å/pix.
x 296 pix.
= 184.112 Å		0.62 Å/pix.
x 296 pix.
= 184.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.622 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0475
Minimum - Maximum-0.19551623 - 0.31059477
Average (Standard dev.)0.00008580772 (±0.010805764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions296296296
Spacing296296296
CellA=B=C: 184.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : alpha1/beta tubulin heterodimer

EntireName: alpha1/beta tubulin heterodimer
Components
  • Complex: alpha1/beta tubulin heterodimer
    • Complex: Tubulin alpha-1 chain
      • Protein or peptide: Tubulin alpha-1 chain
    • Complex: Tubulin beta-1 chain
      • Protein or peptide: Tubulin beta-1 chain
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: alpha1/beta tubulin heterodimer

SupramoleculeName: alpha1/beta tubulin heterodimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Tubulin alpha-1 chain

SupramoleculeName: Tubulin alpha-1 chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Supramolecule #3: Tubulin beta-1 chain

SupramoleculeName: Tubulin beta-1 chain / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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Macromolecule #1: Tubulin alpha-1 chain

MacromoleculeName: Tubulin alpha-1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / 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: 1 / Enantiomer: LEVO
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 50.194137 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEIISDEHGI DATGAYHGDS DLQLERINVY YNEASGGKYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTYS ...String:
MREIVHIQAG QCGNQIGAKF WEIISDEHGI DATGAYHGDS DLQLERINVY YNEASGGKYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTYS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSLTMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNIQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QEATADEDAE FEEEQEAEVD EN

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: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / 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: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.9
GridModel: UltrAuFoil R2/2 / Material: GOLD / Mesh: 200
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 5724 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2q1t

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 69000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2q1t


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

PDB-7quc:
D. melanogaster alpha/beta tubulin heterodimer in the GDP form

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