9S7G | pdb_00009s7g

SPACA9 and MNMIP1 bound to the seam of manchette microtubules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

SPACA9 and MNMIP1 bridge the seam of spermatid manchette microtubules.

Judernatz, J.H.Doroshev, S.Hoogebeen, R.A.Jonkers, S.Schweizer, D.Gravett, M.S.C.Bromfield, E.G.Howes, S.C.Akhmanova, A.Zhang, R.Zeev-Ben-Mordehai, T.

(2026) EMBO J 45: 5024-5045

  • DOI: https://doi.org/10.1038/s44318-026-00833-w
  • Primary Citation Related Structures: 
    9S7G

  • PubMed 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 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.


  • Organizational Affiliation
    • Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 220.66 kDa 
  • Atom Count: 15,323 
  • Modeled Residue Count: 1,929 
  • Deposited Residue Count: 1,949 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin beta-4B chainA [auth B],
C [auth D]
426Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q6P9T8 (Rattus norvegicus)
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Go to UniProtKB:  Q6P9T8
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UniProt GroupQ6P9T8
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Tubulin alpha-1A chainB [auth A],
D [auth C]
437Rattus norvegicusMutation(s): 0 
EC: 3.6.5
UniProt
Find proteins for P68370 (Rattus norvegicus)
Explore P68370 
Go to UniProtKB:  P68370
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UniProt GroupP68370
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Sperm acrosome-associated protein 9159Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for Q4V8P4 (Rattus norvegicus)
Explore Q4V8P4 
Go to UniProtKB:  Q4V8P4
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UniProt GroupQ4V8P4
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
SH3 domain containing 2164Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for F6PUS4 (Rattus norvegicus)
Explore F6PUS4 
Go to UniProtKB:  F6PUS4
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UniProt GroupF6PUS4
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.6

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101088673

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-17
    Type: Initial release
  • Version 1.1: 2026-06-24
    Changes: Data collection, Database references
  • Version 1.2: 2026-07-29
    Changes: Data collection, Database references