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- EMDB-45101: XMAP215-decorated GMPCPP microtubule -

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Basic information

Entry
Database: EMDB / ID: EMD-45101
TitleXMAP215-decorated GMPCPP microtubule
Map data
Sample
  • Complex: XMAP215 TOG5 domain and bovine alpha-beta tubulin
    • Protein or peptide: Bovine tubulin alpha 1a
    • Protein or peptide: Bovine Tubulin beta-2B
    • Protein or peptide: XMAP215 TOG5
KeywordsTOG / microtubule / CELL CYCLE
Function / homology
Function and homology information


microtubule plus end polymerase / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation ...microtubule plus end polymerase / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / establishment or maintenance of microtubule cytoskeleton polarity / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / microtubule nucleation / microtubule plus-end binding / gamma-tubulin binding / positive regulation of axon guidance / microtubule polymerization / centrosome duplication / microtubule-based process / mitotic spindle organization / kinetochore / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / spindle pole / mitotic cell cycle / microtubule cytoskeleton / microtubule binding / microtubule / hydrolase activity / protein heterodimerization activity / cell division / GTPase activity / centrosome / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site ...XMAP215 family / : / XMAP215/Dis1/CLASP, TOG domain / TOG domain / TOG / HEAT repeat profile. / HEAT, type 2 / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Tubulin alpha chain / Tubulin beta-2B chain / Cytoskeleton-associated protein 5-A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.33 Å
AuthorsMcManus CT / Travis SM / Zhang R / Petry S
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM141100-01A1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32 GM142149-01A1 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01 GM141100-01A1 United States
CitationJournal: To Be Published
Title: Structure and function of XMAP215s Cterminal domains in microtubule nucleation
Authors: McManus CT / Travis SM / Jeffrey PD / Zhang R / Petry S
History
DepositionMay 28, 2024-
Header (metadata) releaseMay 28, 2025-
Map releaseMay 28, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45101.png

Downloads & links

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Map

FileDownload / File: emd_45101.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 400 pix.
= 562.12 Å		1.41 Å/pix.
x 400 pix.
= 562.12 Å		1.41 Å/pix.
x 400 pix.
= 562.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4053 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.075
Minimum - Maximum-0.42662805 - 1.000952
Average (Standard dev.)0.0021363937 (±0.06181427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 562.12 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45101_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45101_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_45101_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : XMAP215 TOG5 domain and bovine alpha-beta tubulin

EntireName: XMAP215 TOG5 domain and bovine alpha-beta tubulin
Components
  • Complex: XMAP215 TOG5 domain and bovine alpha-beta tubulin
    • Protein or peptide: Bovine tubulin alpha 1a
    • Protein or peptide: Bovine Tubulin beta-2B
    • Protein or peptide: XMAP215 TOG5

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Supramolecule #1: XMAP215 TOG5 domain and bovine alpha-beta tubulin

SupramoleculeName: XMAP215 TOG5 domain and bovine alpha-beta tubulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 239 kDa/nm

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Macromolecule #1: Bovine tubulin alpha 1a

MacromoleculeName: Bovine tubulin alpha 1a / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Tissue: Brain
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha chain

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Macromolecule #2: Bovine Tubulin beta-2B

MacromoleculeName: Bovine Tubulin beta-2B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VMPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDSK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA

UniProtKB: Tubulin beta-2B chain

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Macromolecule #3: XMAP215 TOG5

MacromoleculeName: XMAP215 TOG5 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: GKEQRVKDEK ALKVLKWNFT TPRDEYIEQL KTQMSPCIAR WLQDELFHAD FQRQIKGLAV MTEHLESEKE GVISCLDLVL KWFTLRFFD TNTSVLMKCL EYLKLLFIML SQEEYHLTEM EGTSFLPYLM LKVGEPKDIV RKDVRAILTK MCQVYPASKM F NFVMEGTK ...String:
GKEQRVKDEK ALKVLKWNFT TPRDEYIEQL KTQMSPCIAR WLQDELFHAD FQRQIKGLAV MTEHLESEKE GVISCLDLVL KWFTLRFFD TNTSVLMKCL EYLKLLFIML SQEEYHLTEM EGTSFLPYLM LKVGEPKDIV RKDVRAILTK MCQVYPASKM F NFVMEGTK SKNSKQRAEC LEELGCLVES YGMNVCQPTP AKALKEIAIH IGDRDTTVRN AALNTIVTVY NVHGEQVFKL IG NLSEKDM SMLEERIKRA GKK

UniProtKB: Cytoskeleton-associated protein 5-A

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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: 6.8
Component:
ConcentrationFormulaName
1.0 mMMgCl2magnesium chloride
80.0 mMC8H18N2O6S2PIPES
0.05 % w/vC58H114O26Tween-20
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00037 kPa / Details: 10mAmp
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 293 K / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-32 / Number grids imaged: 1 / Number real images: 2486 / Average exposure time: 4.1 sec. / Average electron dose: 15.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.1 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

7973


Details: The initial model was low-pass filtered to 20 A resolution.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.33 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 143086
Initial angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.3.2) / Details: projection matching
Final angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC (ver. 3.3.2)
Details: 158,259 particles for 14-PF microtubule, 69,812 particles for 13-PF microtubule,
FSC plot (resolution estimation)

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