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- PDB-9c13: XMAP215 TOG5 interaction with GMPCPP tubulin lattice -

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Basic information

Entry
Database: PDB / ID: 9c13
TitleXMAP215 TOG5 interaction with GMPCPP tubulin lattice
Components
  • Cytoskeleton-associated protein 5-A,Cytoskeleton-associated protein 5-A,Green fluorescent protein
  • Tubulin alpha chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / TOG / microtubule
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
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / 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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsMcManus, C.T. / Travis, S.M. / Jeffrey, P.D. / Zhang, R. / Petry, S.
Funding support United States, 3items
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 C terminal domains in microtubule nucleation
Authors: McManus, C.T. / Travis, S.M. / Jeffrey, P.D. / Zhang, R. / Petry, S.
History
DepositionMay 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Tubulin beta-2B chain
D: Tubulin beta-2B chain
A: Tubulin alpha chain
C: Tubulin alpha chain
E: Cytoskeleton-associated protein 5-A,Cytoskeleton-associated protein 5-A,Green fluorescent protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,30313
Polymers262,1175
Non-polymers2,1868
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 5 molecules BDACE

#1: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Brain / References: UniProt: Q6B856
#2: Protein Tubulin alpha chain


Mass: 50188.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: Brain / References: UniProt: F2Z4C1
#3: Protein Cytoskeleton-associated protein 5-A,Cytoskeleton-associated protein 5-A,Green fluorescent protein / Microtubule-associated protein 215 kDa / XMAP215


Mass: 61740.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: ckap5-a, xmap215, GFP / Plasmid: pST50 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9PT63

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Non-polymers , 3 types, 8 molecules

#4: Chemical ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM

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Details

Has ligand of interestN
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: XMAP215 TOG5 and bovine alpha-beta tubulin / Type: COMPLEX / Entity ID: #1-#3 / Source: MULTIPLE SOURCES
Molecular weightValue: 239 kDa/nm / Experimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21 / Plasmid: pST50
Buffer solutionpH: 6.8
Buffer component
IDConc.NameFormulaBuffer-ID
11 mMmagnesium chlorideMgCl21
280 mMPIPESC8H18N2O6S21
30.05 % w/vTween-20C58H114O261
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 10mAmp / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 293 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm / Cs: 0.1 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 4.1 sec. / Electron dose: 15 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 2486
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV
Image scansWidth: 3710 / Height: 3838 / Movie frames/image: 32 / Used frames/image: 1-32

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Processing

EM software
IDNameVersionCategory
2EPU2.12.1.2782RELimage acquisition
4cryoSPARC3.3.2CTF correction
7Coot0.8.9.2model fitting
9PHENIX1.21-5207-000model refinement
10cryoSPARC3.3.2initial Euler assignment
11cryoSPARC3.3.2final Euler assignment
12cryoSPARC3.3.2classification
13cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -25.75 ° / Axial rise/subunit: 9.012 Å / Axial symmetry: C1
3D reconstructionResolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 334570 / Algorithm: FOURIER SPACE
Details: Symmetry expansion was used based on microtubule pseudo-helical symmetry.
Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Accession code: 6DPU / Initial refinement model-ID: 2 / PDB-ID: 6DPU

6dpu

/ Source name: PDB / Type: experimental model

IDPdb chain-IDChain-ID
1BB
2JJ
3FF
4KK
RefinementHighest resolution: 2.89 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00543769
ELECTRON MICROSCOPYf_angle_d0.84359438
ELECTRON MICROSCOPYf_dihedral_angle_d6.055978
ELECTRON MICROSCOPYf_chiral_restr0.0556507
ELECTRON MICROSCOPYf_plane_restr0.0077719

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