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- PDB-9s7g: SPACA9 and MNMIP1 bound to the seam of manchette microtubules -

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Basic information

Entry
Database: PDB / ID: 9s7g
TitleSPACA9 and MNMIP1 bound to the seam of manchette microtubules
Components
  • SH3 domain containing 21
  • Sperm acrosome-associated protein 9
  • Tubulin alpha-1A chain
  • Tubulin beta-4B chain
KeywordsCYTOSOLIC PROTEIN / Microtubule
Function / homology
Function and homology information


Cargo trafficking to the periciliary membrane / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / RHO GTPases activate IQGAPs / PKR-mediated signaling / Intraflagellar transport / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Resolution of Sister Chromatid Cohesion ...Cargo trafficking to the periciliary membrane / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / RHO GTPases activate IQGAPs / PKR-mediated signaling / Intraflagellar transport / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / internode region of axon / axonemal microtubule doublet inner sheath / Regulation of PLK1 Activity at G2/M Transition / Separation of Sister Chromatids / Hedgehog 'off' state / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / netrin-activated signaling pathway / netrin receptor binding / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / axoneme assembly / MHC class II antigen presentation / odontoblast differentiation / dorsal root ganglion development / axonemal microtubule / organelle transport along microtubule / Recycling pathway of L1 / forebrain morphogenesis / glial cell differentiation / cerebellar cortex morphogenesis / dentate gyrus development / neuron projection arborization / smoothened signaling pathway / pyramidal neuron differentiation / motor behavior / response to L-glutamate / GTPase activating protein binding / centrosome cycle / Neutrophil degranulation / adult behavior / 'de novo' protein folding / startle response / flagellated sperm motility / ciliary base / nuclear envelope lumen / negative regulation of microtubule polymerization / regulation of synapse organization / microtubule polymerization / locomotory exploration behavior / response to tumor necrosis factor / MHC class I protein binding / homeostasis of number of cells within a tissue / response to mechanical stimulus / axoneme / sperm flagellum / adult locomotory behavior / microtubule-based process / neurogenesis / cytoplasmic microtubule / condensed chromosome / spindle assembly / cell projection / peptide binding / cellular response to calcium ion / axon guidance / acrosomal vesicle / hippocampus development / locomotory behavior / cell periphery / sperm end piece / filopodium / neuromuscular junction / neuron migration / visual learning / cerebral cortex development / intracellular protein transport / memory / synapse organization / microtubule cytoskeleton organization / recycling endosome / gene expression / structural constituent of cytoskeleton / neuron differentiation / cytoplasmic ribonucleoprotein granule / calcium-dependent protein binding / neuron apoptotic process / microtubule cytoskeleton / myelin sheath / mitotic cell cycle
Similarity search - Function
SH3D21, SH3 domain / Sperm acrosome-associated protein 9 / Sperm acrosome-associated protein 9 / : / Variant SH3 domain / Variant SH3 domain / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin ...SH3D21, SH3 domain / Sperm acrosome-associated protein 9 / Sperm acrosome-associated protein 9 / : / Variant SH3 domain / Variant SH3 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / SH3 domain containing 21 / Tubulin alpha-1A chain / Sperm acrosome-associated protein 9 / Tubulin beta-4B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJudernatz, J.H. / Zhang, R. / Zeev-Ben-Mordehai, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)101088673European Union
CitationJournal: EMBO J / Year: 2026
Title: SPACA9 and MNMIP1 bridge the seam of spermatid manchette microtubules.
Authors: Jo H Judernatz / Svetlana Doroshev / Robin A Hoogebeen / Sven Jonkers / Donna Schweizer / Molly S C Gravett / Elizabeth G Bromfield / Stuart C Howes / Anna Akhmanova / Rui Zhang / Tzviya Zeev-Ben-Mordehai /
Abstract: The manchette is a transient microtubule (MT)-based structure that is vital for the correct shaping of sperm during spermiogenesis. Throughout spermiogenesis, the manchette retains structural ...The manchette is a transient microtubule (MT)-based structure that is vital for the correct shaping of sperm during spermiogenesis. Throughout spermiogenesis, the manchette retains structural integrity for several days, raising the question of how its MTs are regulated. Here, using cryo-electron tomography of manchettes isolated from rat testes, we find that manchette MT ends are structurally diverse. We show that the MT-binding protein CLASP2 is present throughout the manchette and likely regulates both MT ends. Using cryo-electron microscopy single particle analysis and super-resolution microscopy, we reveal that SPACA9 and MNMIP1 (SH3D21) bind to the seam of manchette MTs from the luminal side. SPACA9 binds to both α- and β-tubulin of protofilament 1 but does not interact directly with protofilament 13, while MNMIP1 binds directly to protofilament 13. MNMIP1 further extends and threads through the MT lattice at the seam. Our study reveals a novel seam MT inner protein complex with a unique binding mode, providing a plausible explanation for MT regulation that maintains manchette integrity over an extended period.
History
DepositionAug 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: 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-4B chain
A: Tubulin alpha-1A chain
D: Tubulin beta-4B chain
C: Tubulin alpha-1A chain
E: Sperm acrosome-associated protein 9
F: SH3 domain containing 21
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,66212
Polymers218,6806
Non-polymers1,9816
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 4 types, 6 molecules BDACEF

#1: Protein Tubulin beta-4B chain / Tubulin beta-2C chain


Mass: 47752.809 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P9T8
#2: Protein Tubulin alpha-1A chain / Alpha-tubulin 1 / Tubulin alpha-1 chain


Mass: 48649.023 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat)
References: UniProt: P68370, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
#3: Protein Sperm acrosome-associated protein 9


Mass: 18470.178 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q4V8P4
#4: Protein SH3 domain containing 21


Mass: 7406.498 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: F6PUS4

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Non-polymers , 3 types, 6 molecules

#5: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#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
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Complex of SPACA9 and MNMIP1 bound to the seam of microtubules
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: #1-#4 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1137 mMSodium chlorideNaCl1
22.7 mMPotassium chlorideKCl1
310 mMSodium Phosphate DibasicNa2HPO41
41.8 mMPotassium Phosphate MonobasicKH2PO41
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 79000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 8 / Num. of real images: 7598

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.6particle selection
2PHENIX1.21.2_5419model refinement
13cryoSPARC4.63D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 971980 / Symmetry type: POINT
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415746
ELECTRON MICROSCOPYf_angle_d0.66121374
ELECTRON MICROSCOPYf_dihedral_angle_d10.1092185
ELECTRON MICROSCOPYf_chiral_restr0.0442339
ELECTRON MICROSCOPYf_plane_restr0.0052779

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