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- PDB-9tmn: Human sperm 20S proteasome complex isolated from native source -

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Entry
Database: PDB / ID: 9tmn
TitleHuman sperm 20S proteasome complex isolated from native source
Components
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Isoform 3 of Proteasome subunit alpha-type 8
  • tripeptide
KeywordsNUCLEAR PROTEIN / proteasome / proteolysis / Ntn hydrolase-like / protein degradation
Function / homology
Function and homology information


regulation of meiosis I / purine ribonucleoside triphosphate binding / structural constituent of proteasome / CD8-positive, alpha-beta T cell differentiation / CD8-positive, alpha-beta T cell homeostasis / thymic T cell selection / Antigen processing: Ub, ATP-independent proteasomal degradation / spermatoproteasome complex / negative regulation of regulatory T cell differentiation / T-helper 1 cell differentiation ...regulation of meiosis I / purine ribonucleoside triphosphate binding / structural constituent of proteasome / CD8-positive, alpha-beta T cell differentiation / CD8-positive, alpha-beta T cell homeostasis / thymic T cell selection / Antigen processing: Ub, ATP-independent proteasomal degradation / spermatoproteasome complex / negative regulation of regulatory T cell differentiation / T-helper 1 cell differentiation / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Proteasome assembly / cellular response to type I interferon / T-helper 17 cell differentiation / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / flagellated sperm motility / sperm end piece / myofibril / Activation of STAT3 by cadherin engagement / ciliary tip / proteasomal ubiquitin-independent protein catabolic process / proteasome storage granule / proteasome endopeptidase complex / NF-kappaB binding / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasome assembly / immune system process / regulation of G1/S transition of mitotic cell cycle / positive regulation of interleukin-2 production / proteasome complex / : / response to type II interferon / regulation of proteasomal protein catabolic process / protein catabolic process / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / negative regulation of inflammatory response to antigenic stimulus / Autodegradation of Cdh1 by Cdh1:APC/C / proteasomal protein catabolic process / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / lipopolysaccharide binding / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / positive regulation of type II interferon production / P-body / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of DVL / Degradation of AXIN / Degradation of CRY and PER proteins / meiotic cell cycle / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Regulation of RUNX3 expression and activity / Autodegradation of the E3 ubiquitin ligase COP1 / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / response to virus / AMPK-induced ERAD and lysosome mediated degradation of PD-L1(CD274) / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Vif-mediated degradation of APOBEC3G / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / GSK3B-mediated proteasomal degradation of PD-L1(CD274) / Degradation of CDH1 / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / ABC-family protein mediated transport / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / SPOP-mediated proteasomal degradation of PD-L1(CD274) / nuclear matrix / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RUNX2 expression and activity / Regulation of RAS by GAPs / positive regulation of tumor necrosis factor production
Similarity search - Function
Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit ...Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-3 ...Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / Proteasome subunit alpha-type 8 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.85 Å
AuthorsKolata, P. / Allegretti, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/30 United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2026
Title: Molecular architecture and spatial organization of proteasomes in the human sperm nucleus
Authors: Kolata, P. / dos Santos, A. / Knowles, O. / Dendooven, T. / Allegretti, M.
History
DepositionDec 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 9, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteasome subunit alpha type-6
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-4
D: Isoform 3 of Proteasome subunit alpha-type 8
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-1
G: Proteasome subunit alpha type-3
H: Proteasome subunit beta type-6
I: Proteasome subunit beta type-7
J: Proteasome subunit beta type-3
K: Proteasome subunit beta type-2
M: Proteasome subunit beta type-1
N: Proteasome subunit beta type-4
O: Proteasome subunit alpha type-6
P: Proteasome subunit alpha type-2
Q: Proteasome subunit alpha type-4
S: Proteasome subunit alpha type-5
U: Proteasome subunit alpha type-3
V: Proteasome subunit beta type-6
W: Proteasome subunit beta type-7
X: Proteasome subunit beta type-3
R: Isoform 3 of Proteasome subunit alpha-type 8
b: Proteasome subunit beta type-4
L: Proteasome subunit beta type-5
a: Proteasome subunit beta type-1
T: Proteasome subunit alpha type-1
Y: Proteasome subunit beta type-2
d: tripeptide
e: tripeptide
Z: Proteasome subunit beta type-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)718,48533
Polymers718,41230
Non-polymers733
Water52,6222921
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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Proteasome subunit alpha type- ... , 6 types, 12 molecules AOBPCQESFTGU

#1: Protein Proteasome subunit alpha type-6 / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota ...27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27432.459 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis / References: UniProt: P60900
#2: Protein Proteasome subunit alpha type-2 / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25927.535 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis / References: UniProt: P25787
#3: Protein Proteasome subunit alpha type-4 / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / ...Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29525.842 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis / References: UniProt: P25789
#5: Protein Proteasome subunit alpha type-5 / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26435.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis / References: UniProt: P28066
#6: Protein Proteasome subunit alpha type-1 / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex ...30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 29595.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis / References: UniProt: P25786
#7: Protein Proteasome subunit alpha type-3 / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28469.252 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis / References: UniProt: P25788

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Proteasome subunit beta type- ... , 7 types, 14 molecules HVIWJXKYMaNbLZ

#8: Protein Proteasome subunit beta type-6 / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / ...Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 21921.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis
References: UniProt: P28072, proteasome endopeptidase complex
#9: Protein Proteasome subunit beta type-7 / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 25321.980 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis
References: UniProt: Q99436, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22972.896 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis
References: UniProt: P49720, proteasome endopeptidase complex
#11: Protein Proteasome subunit beta type-2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22864.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis
References: UniProt: P49721, proteasome endopeptidase complex
#12: Protein Proteasome subunit beta type-1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / ...Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 23578.986 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis
References: UniProt: P20618, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex ...26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 24414.740 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis
References: UniProt: P28070, proteasome endopeptidase complex
#14: Protein Proteasome subunit beta type-5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / ...Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


Mass: 22484.369 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis
References: UniProt: P28074, proteasome endopeptidase complex

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Protein / Protein/peptide , 2 types, 4 molecules DRde

#15: Protein/peptide tripeptide


Mass: 373.471 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis
#4: Protein Isoform 3 of Proteasome subunit alpha-type 8 / Proteasome alpha 4 subunit / Alpha4s / Proteasome subunit alpha-type 7-like


Mass: 27886.977 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: testis / References: UniProt: Q8TAA3

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Non-polymers , 2 types, 2924 molecules

#16: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2921 / Source method: isolated from a natural source / Formula: H2O

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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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Human sperm 20S proteasome / Type: COMPLEX
Details: The native complex was isolated from human spermatozoa.
Entity ID: #1-#15 / Source: NATURAL
Molecular weightValue: 0.7 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human) / Organ: testes
Buffer solutionpH: 7.4
Details: 25 mM HEPES pH 7.4, 100 mM NaCl, 1 mM ATP, 1 mM DTT, 5 mM MgCl2
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPES1
25 mMmagnesium chlorideMgCl21
3100 mMsodium chlorideNaCl1
41 mMDTT1
51 mMATP1
SpecimenConc.: 0.05 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3 sec. / Electron dose: 40 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLO1.9.7particle selection
2PHENIX2.0_5884model refinement
3EPUimage acquisition
5CTFFIND4.1CTF correction
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
12cryoSPARC4.4.1classification
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 896000
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 1.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 222000 / Symmetry type: POINT
Atomic model buildingB value: 32 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: cross-correlation coefficient
Atomic model buildingPDB-ID: 6RGQ

6rgq


Accession code: 6RGQ / Source name: PDB / Type: experimental model
RefinementCross valid method: NONE

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