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- EMDB-54641: SPACA9 and MNMIP1 bound to the seam of manchette microtubules -

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Entry
Database: EMDB / ID: EMD-54641
TitleSPACA9 and MNMIP1 bound to the seam of manchette microtubules
Map data
Sample
  • Organelle or cellular component: Complex of SPACA9 and MNMIP1 bound to the seam of microtubules
    • Protein or peptide: Tubulin beta-4B chain
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Sperm acrosome-associated protein 9
    • Protein or peptide: SH3 domain containing 21
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsMicrotubule / CYTOSOLIC PROTEIN
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsJudernatz JH / Zhang R / Zeev-Ben-Mordehai T
Funding supportEuropean Union, 1 items
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, 2025-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJul 29, 2026-
Current statusJul 29, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_54641.png

Downloads & links

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Map

FileDownload / File: emd_54641.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å		1.32 Å/pix.
x 400 pix.
= 528. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.062343128 - 2.2340245
Average (Standard dev.)0.0028581582 (±0.029904468)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 528.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_54641_msk_1.map
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Half map: half A

Fileemd_54641_half_map_1.map
Annotationhalf A
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Half map: half B

Fileemd_54641_half_map_2.map
Annotationhalf B
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Sample components

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Entire : Complex of SPACA9 and MNMIP1 bound to the seam of microtubules

EntireName: Complex of SPACA9 and MNMIP1 bound to the seam of microtubules
Components
  • Organelle or cellular component: Complex of SPACA9 and MNMIP1 bound to the seam of microtubules
    • Protein or peptide: Tubulin beta-4B chain
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Sperm acrosome-associated protein 9
    • Protein or peptide: SH3 domain containing 21
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of SPACA9 and MNMIP1 bound to the seam of microtubules

SupramoleculeName: Complex of SPACA9 and MNMIP1 bound to the seam of microtubules
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Macromolecule #1: Tubulin beta-4B chain

MacromoleculeName: Tubulin beta-4B chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 47.752809 KDa
SequenceString: MREIVHLQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGKYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHLQAG QCGNQIGAKF WEVISDEHGI DPTGTYHGDS DLQLERINVY YNEATGGKYV PRAVLVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKEAESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTA CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY Q

UniProtKB: Tubulin beta-4B 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: 2 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 48.649023 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 GV

UniProtKB: Tubulin alpha-1A chain

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Macromolecule #3: Sperm acrosome-associated protein 9

MacromoleculeName: Sperm acrosome-associated protein 9 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 18.470178 KDa
SequenceString:
MNEVKESLRS IEQKYKLFQQ QQFTFIAALE HCRENAHDKI RPISSIEQVQ SYMEHYCNNS TDRRILLMFM DICSELNKLC QHFEALHSG TPVTNSLLEK CKTLVSQSND LSILRAKYPH DVVNHLSCDE ARNHYGGVVS LIPIVLDLMK EWIAHSEKLP

UniProtKB: Sperm acrosome-associated protein 9

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Macromolecule #4: SH3 domain containing 21

MacromoleculeName: SH3 domain containing 21 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 7.406498 KDa
SequenceString:
ETCRVLFDYQ PEAPDELALQ KGDLVKVLRK TTEDKGWWEG ECQGRRGVFP DNFVIPPPPI RKLI

UniProtKB: SH3 domain containing 21

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Macromolecule #5: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / 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 #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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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium chloride
2.7 mMKClPotassium chloride
10.0 mMNa2HPO4Sodium Phosphate Dibasic
1.8 mMKH2PO4Potassium Phosphate Monobasic
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 8 / Number real images: 7598 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 79000
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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6) / Number images used: 971980
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER

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