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- EMDB-45100: XMAP215 TOG5 interaction with GMPCPP tubulin lattice -

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Basic information

Entry
Database: EMDB / ID: EMD-45100
TitleXMAP215 TOG5 interaction with GMPCPP tubulin lattice
Map data
Sample
  • Complex: XMAP215 TOG5 and bovine alpha-beta tubulin
    • Protein or peptide: Tubulin beta-2B chain
    • Protein or peptide: Tubulin alpha chain
    • Protein or peptide: Cytoskeleton-associated protein 5-A,Cytoskeleton-associated protein 5-A,Green fluorescent protein
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
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)
Methodhelical reconstruction / cryo EM / Resolution: 2.89 Å
AuthorsMcManus CT / Travis SM / Jeffrey PD / 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 C terminal domains in microtubule nucleation
Authors: McManus CT / Travis SM / Jeffrey PD / Zhang R / Petry S
History
DepositionMay 28, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45100.png

Downloads & links

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Map

FileDownload / File: emd_45100.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: 0.225
Minimum - Maximum-0.6966554 - 1.8578116
Average (Standard dev.)0.0020849276 (±0.051162757)
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_45100_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: J203 DeepEMhancer map

Fileemd_45100_additional_1.map
AnnotationJ203 DeepEMhancer map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Additional map: J203 Bfactor sharpened map

Fileemd_45100_additional_2.map
AnnotationJ203 Bfactor sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: J203 A half map rescaled in relion

Fileemd_45100_half_map_1.map
AnnotationJ203 A half map rescaled in relion
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: J203 half map b rescaled in relion

Fileemd_45100_half_map_2.map
AnnotationJ203 half map b rescaled in relion
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 and bovine alpha-beta tubulin

EntireName: XMAP215 TOG5 and bovine alpha-beta tubulin
Components
  • Complex: XMAP215 TOG5 and bovine alpha-beta tubulin
    • Protein or peptide: Tubulin beta-2B chain
    • Protein or peptide: Tubulin alpha chain
    • Protein or peptide: Cytoskeleton-associated protein 5-A,Cytoskeleton-associated protein 5-A,Green fluorescent protein
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE

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

SupramoleculeName: XMAP215 TOG5 and bovine alpha-beta tubulin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 239 kDa/nm

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Macromolecule #1: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: Brain
Molecular weightTheoretical: 49.999887 KDa
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 #2: Tubulin alpha chain

MacromoleculeName: Tubulin alpha chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle) / Organ: Brain
Molecular weightTheoretical: 50.188441 KDa
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 #3: Cytoskeleton-associated protein 5-A,Cytoskeleton-associated prote...

MacromoleculeName: Cytoskeleton-associated protein 5-A,Cytoskeleton-associated protein 5-A,Green fluorescent protein
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 61.740691 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGPIYIIVPN GKEQRVKDEK ALKVLKWNFT TPRDEYIEQL KTQMSPCIAR WLQDELFHAD FQRQIKGLAV MTEHLESEKE GVISCLDLV LKWFTLRFFD TNTSVLMKCL EYLKLLFIML SQEEYHLTEM EGTSFLPYLM LKVGEPKDIV RKDVRAILTK M CQVYPASK ...String:
MGPIYIIVPN GKEQRVKDEK ALKVLKWNFT TPRDEYIEQL KTQMSPCIAR WLQDELFHAD FQRQIKGLAV MTEHLESEKE GVISCLDLV LKWFTLRFFD TNTSVLMKCL EYLKLLFIML SQEEYHLTEM EGTSFLPYLM LKVGEPKDIV RKDVRAILTK M CQVYPASK MFNFVMEGTK SKNSKQRAEC LEELGCLVES YGMNVCQPTP AKALKEIAIH IGDRDTTVRN AALNTIVTVY NV HGEQVFK LIGNLSEKDM SMLEERIKRA GKKQAPYVDG GAATMVSKGE ELFTGVVPIL VELDGDVNGH KFSVSGEGEG DAT YGKLTL KFICTTGKLP VPWPTLVTTL TYGVQCFSRY PDHMKQHDFF KSAMPEGYVQ ERTIFFKDDG NYKTRAEVKF EGDT LVNRI ELKGIDFKED GNILGHKLEY NYNSHNVYIM ADKQKNGIKV NFKIRHNIED GSVQLADHYQ QNTPIGDGPV LLPDN HYLS TQSALSKDPN EKRDHMVLKE FVTAAGITLG MDELYKVDHH HHHHHPGSAW SHPQFEK

UniProtKB: Cytoskeleton-associated protein 5-A

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Macromolecule #4: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / type: ligand / ID: 4 / Number of copies: 2 / Formula: G2P
Molecular weightTheoretical: 521.208 Da
Chemical component information

ChemComp-G2P:
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / GMP-CPP, energy-carrying molecule analogue*YM

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical 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

MicroscopeTFS 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

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 9.012 Å
Applied symmetry - Helical parameters - Δ&Phi: -25.75 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.89 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2)
Details: Symmetry expansion was used based on microtubule pseudo-helical symmetry.
Number images used: 334570
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 angle assignmentType: NOT APPLICABLE / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6dpu

chain_id: B, source_name: PDB, initial_model_type: experimental model

6dpu

chain_id: J, source_name: PDB, initial_model_type: experimental model

6dpu

chain_id: F, source_name: PDB, initial_model_type: experimental model

6dpu

chain_id: K, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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