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- EMDB-54112: CryoEM structure of the microtubule-AKAP13 C1 domain complex -

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Basic information

Entry
Database: EMDB / ID: EMD-54112
TitleCryoEM structure of the microtubule-AKAP13 C1 domain complex
Map dataC1 domain of AKAP13 bound to microtubules
Sample
  • Complex: Complex of C1 domain of AKAP13 with microtubules
    • Complex: C1 domain of AKAP13
    • Complex: Microtubules
KeywordsMicrotubules / AKAP13 / C1 / signaling molecule / SIGNALING PROTEIN
Biological speciesHomo sapiens (human) / Sus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsGiono M / Choi SR / Filipcik P / Steinmetz MO
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Cell / Year: 2026
Title: Structural basis of microtubule-mediated signal transduction.
Authors: Sung Ryul Choi / Thorsten B Blum / Matteo Giono / Bibhas Roy / Ioannis Vakonakis / Dominic Schmid / Nicole Oelgarth / Apisha Ranganathan / Alvar D Gossert / G V Shivashankar / Alfred ...Authors: Sung Ryul Choi / Thorsten B Blum / Matteo Giono / Bibhas Roy / Ioannis Vakonakis / Dominic Schmid / Nicole Oelgarth / Apisha Ranganathan / Alvar D Gossert / G V Shivashankar / Alfred Zippelius / Michel O Steinmetz /
Abstract: Microtubules have long been recognized as upstream mediators of intracellular signaling, but the mechanisms underlying this fundamental function remain elusive. Here, we identify the structural basis ...Microtubules have long been recognized as upstream mediators of intracellular signaling, but the mechanisms underlying this fundamental function remain elusive. Here, we identify the structural basis by which microtubules regulate the guanine nucleotide exchange factor H1 (GEFH1), a key activator of the Ras homolog family member A (RhoA) pathway. We show that specific features of the microtubule lattice bind the C1 domain of GEFH1, leading to the sequestration and inactivation of this signaling protein. Targeted mutations in C1 residues disrupt this interaction, triggering GEFH1 release and activation of RhoA-dependent immune responses. Building on this sequestration-and-release mechanism, we identify microtubule-binding C1 domains in additional signaling proteins, including other guanine nucleotide exchange factors (GEFs), kinases, a GTPase-activating protein (GAP), and a tumor suppressor, and show that microtubule-mediated regulation via C1 domains is conserved in the Ras association domain-containing protein 1A (RASSF1A). Our findings establish a structural framework for understanding how microtubules can function as spatiotemporal signal sensors, integrating and processing diverse signaling pathways to control important cellular processes.
History
DepositionJun 20, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54112.png

Downloads & links

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Map

FileDownload / File: emd_54112.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationC1 domain of AKAP13 bound to microtubules
Voxel sizeX=Y=Z: 1.058 Å
Density
Contour LevelBy AUTHOR: 0.105
Minimum - Maximum-0.30996403 - 0.9781988
Average (Standard dev.)0.0014902214 (±0.019766519)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_54112_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_54112_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 : Complex of C1 domain of AKAP13 with microtubules

EntireName: Complex of C1 domain of AKAP13 with microtubules
Components
  • Complex: Complex of C1 domain of AKAP13 with microtubules
    • Complex: C1 domain of AKAP13
    • Complex: Microtubules

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Supramolecule #1: Complex of C1 domain of AKAP13 with microtubules

SupramoleculeName: Complex of C1 domain of AKAP13 with microtubules / type: complex / ID: 1 / Parent: 0
Molecular weightTheoretical: 8.2 kDa/nm

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Supramolecule #2: C1 domain of AKAP13

SupramoleculeName: C1 domain of AKAP13 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Microtubules

SupramoleculeName: Microtubules / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Sus scrofa (pig)

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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: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClSodium Chloride
20.0 mMTris-HCltris(hydroxymethyl)aminomethane
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.85 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 664267
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: cryoSPARC

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