9TMN | pdb_00009tmn

Human sperm 20S proteasome complex isolated from native source


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Molecular architecture and spatial organization of proteasomes in the human sperm nucleus.

Kolata, P.Dos Santos, A.Knowles, O.Dendooven, T.Allegretti, M.

(2026) Nat Struct Mol Biol 

  • DOI: https://doi.org/10.1038/s41594-026-01870-z
  • Primary Citation Related Structures: 
    9TMN, 9TMS

  • PubMed Abstract: 

    Proteasomes are fundamental for protein homeostasis and genome integrity and essential in spermatogenesis and fertilization. However, their presence, composition and role within the sperm nucleus are a subject of debate. Here we use in situ cryo-electron tomography in human sperm cells to elucidate the molecular architecture of nuclear proteasomes, which cluster in DNA-free, nuclear cavities within the sperm nucleus. We show that the main population of proteasomes consists of 20S core particles, with a smaller fraction of 20S capped by PA200 activator. Using single-particle cryo-electron microscopy of purified native human sperm proteasomes, we elucidate the features of the essential testis-specific subunit α4s, reporting the presence of a unique splice variant. We resolve a native peptide in the catalytic β2 subunit, providing insight into the proteolysis mechanism and PA200-mediated enhancement of trypsin activity. We show nuclear enrichment of proteasomes during sperm-cell differentiation in human testis tissue, with 20S and PA200 clustering following meiosis, at the spermatid stage. Our findings shed light on the organization and compositional diversity of nuclear proteasomes in human sperm cells, as well as their catalytic function.


  • Organizational Affiliation
    • Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, UK.

Macromolecule Content 

  • Total Structure Weight: 718.49 kDa 
  • Atom Count: 51,258 
  • Modeled Residue Count: 6,218 
  • Deposited Residue Count: 6,468 
  • Unique protein chains: 15

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6A,
N [auth O]
246Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P60900 (Homo sapiens)
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PHAROS:  P60900
GTEx:  ENSG00000100902 
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UniProt GroupP60900
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2B,
O [auth P]
234Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P25787 (Homo sapiens)
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PHAROS:  P25787
GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C,
P [auth Q]
261Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P25789 (Homo sapiens)
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PHAROS:  P25789
GTEx:  ENSG00000041357 
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UniProt GroupP25789
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 3 of Proteasome subunit alpha-type 8D,
V [auth R]
250Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TAA3 (Homo sapiens)
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PHAROS:  Q8TAA3
GTEx:  ENSG00000154611 
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UniProt GroupQ8TAA3
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5E,
Q [auth S]
241Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P28066 (Homo sapiens)
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PHAROS:  P28066
GTEx:  ENSG00000143106 
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UniProt GroupP28066
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1F,
Z [auth T]
263Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens)
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GTEx:  ENSG00000129084 
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UniProt GroupP25786
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3G,
R [auth U]
255Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P25788 (Homo sapiens)
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PHAROS:  P25788
GTEx:  ENSG00000100567 
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UniProt GroupP25788
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6H,
S [auth V]
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28072 (Homo sapiens)
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PHAROS:  P28072
GTEx:  ENSG00000142507 
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UniProt GroupP28072
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7I,
T [auth W]
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99436 (Homo sapiens)
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PHAROS:  Q99436
GTEx:  ENSG00000136930 
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UniProt GroupQ99436
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3J,
U [auth X]
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49720 (Homo sapiens)
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PHAROS:  P49720
GTEx:  ENSG00000277791 
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UniProt GroupP49720
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2AA [auth Y],
K
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49721 (Homo sapiens)
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GTEx:  ENSG00000126067 
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UniProt GroupP49721
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1L [auth M],
Y [auth a]
213Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P20618 (Homo sapiens)
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PHAROS:  P20618
GTEx:  ENSG00000008018 
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UniProt GroupP20618
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4M [auth N],
W [auth b]
219Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28070 (Homo sapiens)
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PHAROS:  P28070
GTEx:  ENSG00000159377 
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UniProt GroupP28070
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5DA [auth Z],
X [auth L]
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28074 (Homo sapiens)
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PHAROS:  P28074
GTEx:  ENSG00000100804 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
tripeptideBA [auth d],
CA [auth e]
3Homo sapiensMutation(s): 0 
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.85 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX2.0_5884
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UP_1201/30

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-09
    Type: Initial release
  • Version 1.1: 2026-09-16
    Changes: Data collection, Database references