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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 / Kinesins / Resolution of Sister Chromatid Cohesion / COPI-independent Golgi-to-ER retrograde traffic ...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 / Kinesins / Resolution of Sister Chromatid Cohesion / COPI-independent Golgi-to-ER retrograde traffic / 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 / cerebellar cortex morphogenesis / glial cell differentiation / dentate gyrus development / neuron projection arborization / flagellated sperm motility / pyramidal neuron differentiation / GTPase activating protein binding / response to L-glutamate / Neutrophil degranulation / centrosome cycle / 'de novo' protein folding / smoothened signaling pathway / ciliary base / nuclear envelope lumen / negative regulation of microtubule polymerization / regulation of synapse organization / startle response / motor behavior / adult behavior / microtubule polymerization / locomotory exploration behavior / response to tumor necrosis factor / MHC class I protein binding / axoneme / response to mechanical stimulus / sperm flagellum / microtubule-based process / cytoplasmic microtubule / condensed chromosome / spindle assembly / cell projection / peptide binding / neurogenesis / homeostasis of number of cells within a tissue / cellular response to calcium ion / acrosomal vesicle / axon guidance / cell periphery / filopodium / hippocampus development / adult locomotory behavior / neuromuscular junction / sperm end piece / locomotory behavior / intracellular protein transport / cerebral cortex development / synapse organization / visual learning / structural constituent of cytoskeleton / recycling endosome / microtubule cytoskeleton organization / neuron migration / neuron differentiation / memory / calcium-dependent protein binding / cytoplasmic ribonucleoprotein granule / myelin sheath / mitotic cell cycle / lamellipodium / double-stranded RNA binding / growth cone
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: To Be Published
Title: SPACA9 and MNMIP1 bridge the seam of manchette microtubules
Authors: Judernatz, J.H. / Zhang, R. / Zeev-Ben-Mordehai, T.
History
DepositionAug 4, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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