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- EMDB-70956: In situ microtubule structure in the axon of a human neuron -

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Basic information

Entry
Database: EMDB / ID: EMD-70956
TitleIn situ microtubule structure in the axon of a human neuron
Map dataPost-processed full map.
Sample
  • Complex: Axonal alpha1A and betaIIB microtubule
    • Protein or peptide: Tubulin beta-2B chain
    • Protein or peptide: Tubulin alpha-1A chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: water
KeywordsHuman in-situ microtubule / axon / cytoskeleton / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Post-chaperonin tubulin folding pathway / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / organelle transport along microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport ...Post-chaperonin tubulin folding pathway / axonemal microtubule / Cilium Assembly / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / organelle transport along microtubule / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / glial cell differentiation / dentate gyrus development / neuron projection arborization / embryonic brain development / flagellated sperm motility / Gap junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / positive regulation of axon guidance / Assembly and cell surface presentation of NMDA receptors / pyramidal neuron differentiation / response to L-glutamate / COPI-independent Golgi-to-ER retrograde traffic / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / smoothened signaling pathway / regulation of synapse organization / startle response / motor behavior / microtubule polymerization / Recycling pathway of L1 / locomotory exploration behavior / response to tumor necrosis factor / response to mechanical stimulus / sperm flagellum / microtubule-based process / RHO GTPases activate IQGAPs / Hedgehog 'off' state / intercellular bridge / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / condensed chromosome / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / homeostasis of number of cells within a tissue / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / cellular response to calcium ion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / adult locomotory behavior / Translocation of SLC2A4 (GLUT4) to the plasma membrane / neuromuscular junction / intracellular protein transport / RHO GTPases Activate Formins / cerebral cortex development / synapse organization / PKR-mediated signaling / visual learning / recycling endosome / structural constituent of cytoskeleton / modulation of chemical synaptic transmission / microtubule cytoskeleton organization / Schaffer collateral - CA1 synapse / neuron migration / memory / cytoplasmic ribonucleoprotein granule / HCMV Early Events / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / microtubule cytoskeleton / neuron apoptotic process / gene expression / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / cilium / protein heterodimerization activity / cell division / hydrolase activity / GTPase activity / GTP binding / protein-containing complex binding / structural molecule activity / extracellular exosome / metal ion binding / identical protein binding / nucleus / plasma membrane / 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-1A chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 2.69 Å
AuthorsZehr EA / Sun S / Roll-Mecak A
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)1ZIANS003164 United States
CitationJournal: To Be Published
Title: Microtubules in the axon are GDP-bound but adopt a stable GTP-like expanded state
Authors: Zehr EA / Sun S / Sarbanes SL / Roll-Mecak A
History
DepositionJun 3, 2025-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70956.png

Downloads & links

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Map

FileDownload / File: emd_70956.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed full map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 720 pix.
= 593.28 Å		0.82 Å/pix.
x 720 pix.
= 593.28 Å		0.82 Å/pix.
x 720 pix.
= 593.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.824 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.2542832 - 1.8254218
Average (Standard dev.)0.00073342305 (±0.026359739)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 593.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70956_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw full map.

Fileemd_70956_additional_1.map
AnnotationRaw full map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Full map processed with DeepEMhancer.

Fileemd_70956_additional_2.map
AnnotationFull map processed with DeepEMhancer.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map.

Fileemd_70956_half_map_1.map
AnnotationHalf-map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map.

Fileemd_70956_half_map_2.map
AnnotationHalf-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 : Axonal alpha1A and betaIIB microtubule

EntireName: Axonal alpha1A and betaIIB microtubule
Components
  • Complex: Axonal alpha1A and betaIIB microtubule
    • Protein or peptide: Tubulin beta-2B chain
    • Protein or peptide: Tubulin alpha-1A chain
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: water

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Supramolecule #1: Axonal alpha1A and betaIIB microtubule

SupramoleculeName: Axonal alpha1A and betaIIB microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human) / Tissue: neuronal / Location in cell: axon
Molecular weightTheoretical: 1 MDa

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Macromolecule #1: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Neuronal
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 FEEEEGEDEA

UniProtKB: Tubulin beta-2B chain

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Macromolecule #2: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: Neuronal
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-1A chain

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Macromolecule #3: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

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Macromolecule #4: MAGNESIUM ION

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

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / 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 #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 32 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.55 mg/mL
BufferpH: 7.2
GridModel: Quantifoil R2/2 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 100 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 85 % / Chamber temperature: 303 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 6 / Number real images: 3017 / Average exposure time: 2.03 sec. / Average electron dose: 56.57 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 9.60742 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.6723 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 1887666
CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Segment selectionNumber selected: 288841 / Software - Name: cryoSPARC (ver. 4)
Startup modelType of model: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8v4k


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: ISOLDE (ver. 1.6)
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 69 / Target criteria: cross-correlation
Output model

PDB-9ox7:
In situ microtubule structure in the axon of a human neuron

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