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- EMDB-56074: Human sperm 20S-PA200 proteasome complex isolated from native source -

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Basic information

Entry
Database: EMDB / ID: EMD-56074
TitleHuman sperm 20S-PA200 proteasome complex isolated from native source
Map data
Sample
  • Complex: Human sperm 20S proteasome in complex with PA200 activator
    • Protein or peptide: x 15 types
  • Ligand: x 1 types
Keywordsproteasome / proteolysis / Ntn hydrolase-like / nuclear protein / protein degradation
Function / homology
Function and homology information


regulation of meiosis I / sperm DNA condensation / 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 ...regulation of meiosis I / sperm DNA condensation / 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 / peptidase activator activity / 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 / proteasome binding / 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
Similarity search - Function
Proteasome activator complex subunit 4 C-terminal domain / Proteasome activator Blm10, mid region / Proteasome activator complex subunit 4 / : / Proteasome activator complex subunit 4-like, C-terminal / Proteasome activator complex subunit 4, mid HEAT repeats region / Proteasome activator complex subunit 4-like, HEAT repeat-like / Proteasome subunit alpha 1 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal ...Proteasome activator complex subunit 4 C-terminal domain / Proteasome activator Blm10, mid region / Proteasome activator complex subunit 4 / : / Proteasome activator complex subunit 4-like, C-terminal / Proteasome activator complex subunit 4, mid HEAT repeats region / Proteasome activator complex subunit 4-like, HEAT repeat-like / 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 / Armadillo-like helical / Armadillo-type fold
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 activator complex subunit 4 / Proteasome subunit alpha-type 8 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsKolata P / Allegretti M
Funding support United Kingdom, 1 items
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, 2025-
Header (metadata) releaseSep 9, 2026-
Map releaseSep 9, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56074.png

Downloads & links

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Map

FileDownload / File: emd_56074.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 420 pix.
= 388.92 Å		0.93 Å/pix.
x 420 pix.
= 388.92 Å		0.93 Å/pix.
x 420 pix.
= 388.92 Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.926 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4
Minimum - Maximum-1.1179671 - 1.947385
Average (Standard dev.)0.004698651 (±0.09319371)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 388.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_56074_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56074_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Human sperm 20S proteasome in complex with PA200 activator

EntireName: Human sperm 20S proteasome in complex with PA200 activator
Components
  • Complex: Human sperm 20S proteasome in complex with PA200 activator
    • Protein or peptide: Proteasome subunit alpha type-6
    • Protein or peptide: Proteasome subunit alpha type-2
    • Protein or peptide: Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit beta type-6
    • Protein or peptide: Proteasome subunit beta type-7
    • Protein or peptide: Proteasome subunit beta type-3
    • Protein or peptide: Proteasome subunit beta type-2
    • Protein or peptide: Proteasome subunit beta type-5
    • Protein or peptide: Proteasome subunit beta type-1
    • Protein or peptide: Proteasome subunit beta type-4
    • Protein or peptide: Proteasome subunit alpha type-4
    • Protein or peptide: Isoform 3 of Proteasome subunit alpha-type 8
    • Protein or peptide: Proteasome subunit alpha type-5
    • Protein or peptide: Proteasome activator complex subunit 4
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: Human sperm 20S proteasome in complex with PA200 activator

SupramoleculeName: Human sperm 20S proteasome in complex with PA200 activator
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Details: The native complex was isolated from human spermatozoa.
Source (natural)Organism: Homo sapiens (human) / Organ: testes
Molecular weightTheoretical: 950 KDa

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Macromolecule #1: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 27.432459 KDa
SequenceString: MSRGSSAGFD RHITIFSPEG RLYQVEYAFK AINQGGLTSV AVRGKDCAVI VTQKKVPDKL LDSSTVTHLF KITENIGCVM TGMTADSRS QVQRARYEAA NWKYKYGYEI PVDMLCKRIA DISQVYTQNA EMRPLGCCMI LIGIDEEQGP QVYKCDPAGY Y CGFKATAA ...String:
MSRGSSAGFD RHITIFSPEG RLYQVEYAFK AINQGGLTSV AVRGKDCAVI VTQKKVPDKL LDSSTVTHLF KITENIGCVM TGMTADSRS QVQRARYEAA NWKYKYGYEI PVDMLCKRIA DISQVYTQNA EMRPLGCCMI LIGIDEEQGP QVYKCDPAGY Y CGFKATAA GVKQTESTSF LEKKVKKKFD WTFEQTVETA ITCLSTVLSI DFKPSEIEVG VVTVENPKFR ILTEAEIDAH LV ALAERD

UniProtKB: Proteasome subunit alpha type-6

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Macromolecule #2: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 25.927535 KDa
SequenceString: MAERGYSFSL TTFSPSGKLV QIEYALAAVA GGAPSVGIKA ANGVVLATEK KQKSILYDER SVHKVEPITK HIGLVYSGMG PDYRVLVHR ARKLAQQYYL VYQEPIPTAQ LVQRVASVMQ EYTQSGGVRP FGVSLLICGW NEGRPYLFQS DPSGAYFAWK A TAMGKNYV ...String:
MAERGYSFSL TTFSPSGKLV QIEYALAAVA GGAPSVGIKA ANGVVLATEK KQKSILYDER SVHKVEPITK HIGLVYSGMG PDYRVLVHR ARKLAQQYYL VYQEPIPTAQ LVQRVASVMQ EYTQSGGVRP FGVSLLICGW NEGRPYLFQS DPSGAYFAWK A TAMGKNYV NGKTFLEKRY NEDLELEDAI HTAILTLKES FEGQMTEDNI EVGICNEAGF RRLTPTEVKD YLAAIA

UniProtKB: Proteasome subunit alpha type-2

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Macromolecule #3: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 29.595627 KDa
SequenceString: MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPVSRLV SLIGSKTQIP TQRYGRRPYG VGLLIAGYDD MGPHIFQTCP SANYFDCRAM S IGARSQSA ...String:
MFRNQYDNDV TVWSPQGRIH QIEYAMEAVK QGSATVGLKS KTHAVLVALK RAQSELAAHQ KKILHVDNHI GISIAGLTAD ARLLCNFMR QECLDSRFVF DRPLPVSRLV SLIGSKTQIP TQRYGRRPYG VGLLIAGYDD MGPHIFQTCP SANYFDCRAM S IGARSQSA RTYLERHMSE FMECNLNELV KHGLRALRET LPAEQDLTTK NVSIGIVGKD LEFTIYDDDD VSPFLEGLEE RP QRKAQPA QPADEPAEKA DEPMEH

UniProtKB: Proteasome subunit alpha type-1

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Macromolecule #4: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 28.469252 KDa
SequenceString: MSSIGTGYDL SASTFSPDGR VFQVEYAMKA VENSSTAIGI RCKDGVVFGV EKLVLSKLYE EGSNKRLFNV DRHVGMAVAG LLADARSLA DIAREEASNF RSNFGYNIPL KHLADRVAMY VHAYTLYSAV RPFGCSFMLG SYSVNDGAQL YMIDPSGVSY G YWGCAIGK ...String:
MSSIGTGYDL SASTFSPDGR VFQVEYAMKA VENSSTAIGI RCKDGVVFGV EKLVLSKLYE EGSNKRLFNV DRHVGMAVAG LLADARSLA DIAREEASNF RSNFGYNIPL KHLADRVAMY VHAYTLYSAV RPFGCSFMLG SYSVNDGAQL YMIDPSGVSY G YWGCAIGK ARQAAKTEIE KLQMKEMTCR DIVKEVAKII YIVHDEVKDK AFELELSWVG ELTNGRHEIV PKDIREEAEK YA KESLKEE DESDDDNM

UniProtKB: Proteasome subunit alpha type-3

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Macromolecule #5: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 21.921836 KDa
SequenceString: TTIMAVQFDG GVVLGADSRT TTGSYIANRV TDKLTPIHDR IFCCRSGSAA DTQAVADAVT YQLGFHSIEL NEPPLVHTAA SLFKEMCYR YREDLMAGII IAGWDPQEGG QVYSVPMGGM MVRQSFAIGG SGSSYIYGYV DATYREGMTK EECLQFTANA L ALAMERDG ...String:
TTIMAVQFDG GVVLGADSRT TTGSYIANRV TDKLTPIHDR IFCCRSGSAA DTQAVADAVT YQLGFHSIEL NEPPLVHTAA SLFKEMCYR YREDLMAGII IAGWDPQEGG QVYSVPMGGM MVRQSFAIGG SGSSYIYGYV DATYREGMTK EECLQFTANA L ALAMERDG SSGGVIRLAA IAESGVERQV LLGDQIPKFA VATLPPA

UniProtKB: Proteasome subunit beta type-6

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Macromolecule #6: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 25.32198 KDa
SequenceString: TTIAGVVYKD GIVLGADTRA TEGMVVADKN CSKIHFISPN IYCCGAGTAA DTDMTTQLIS SNLELHSLST GRLPRVVTAN RMLKQMLFR YQGYIGAALV LGGVDVTGPH LYSIYPHGST DKLPYVTMGS GSLAAMAVFE DKFRPDMEEE EAKNLVSEAI A AGIFNDLG ...String:
TTIAGVVYKD GIVLGADTRA TEGMVVADKN CSKIHFISPN IYCCGAGTAA DTDMTTQLIS SNLELHSLST GRLPRVVTAN RMLKQMLFR YQGYIGAALV LGGVDVTGPH LYSIYPHGST DKLPYVTMGS GSLAAMAVFE DKFRPDMEEE EAKNLVSEAI A AGIFNDLG SGSNIDLCVI SKNKLDFLRP YTVPNKKGTR LGRYRCEKGT TAVLTEKITP LEIEVLEETV QTMDTS

UniProtKB: Proteasome subunit beta type-7

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Macromolecule #7: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 22.972896 KDa
SequenceString: MSIMSYNGGA VMAMKGKNCV AIAADRRFGI QAQMVTTDFQ KIFPMGDRLY IGLAGLATDV QTVAQRLKFR LNLYELKEGR QIKPYTLMS MVANLLYEKR FGPYYTEPVI AGLDPKTFKP FICSLDLIGC PMVTDDFVVS GTCAEQMYGM CESLWEPNMD P DHLFETIS ...String:
MSIMSYNGGA VMAMKGKNCV AIAADRRFGI QAQMVTTDFQ KIFPMGDRLY IGLAGLATDV QTVAQRLKFR LNLYELKEGR QIKPYTLMS MVANLLYEKR FGPYYTEPVI AGLDPKTFKP FICSLDLIGC PMVTDDFVVS GTCAEQMYGM CESLWEPNMD P DHLFETIS QAMLNAVDRD AVSGMGVIVH IIEKDKITTR TLKARMD

UniProtKB: Proteasome subunit beta type-3

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Macromolecule #8: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 22.864277 KDa
SequenceString: MEYLIGIQGP DYVLVASDRV AASNIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ ...String:
MEYLIGIQGP DYVLVASDRV AASNIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ KRFILNLPTF SVRIIDKNGI HDLDNISFPK QGS

UniProtKB: Proteasome subunit beta type-2

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Macromolecule #9: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 22.484369 KDa
SequenceString: TTTLAFKFRH GVIVAADSRA TAGAYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQ YKGMGLSMGT MICGWDKRGP GLYYVDSEGN RISGATFSVG SGSVYAYGVM DRGYSYDLEV EQAYDLARRA I YQATYRDA ...String:
TTTLAFKFRH GVIVAADSRA TAGAYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQ YKGMGLSMGT MICGWDKRGP GLYYVDSEGN RISGATFSVG SGSVYAYGVM DRGYSYDLEV EQAYDLARRA I YQATYRDA YSGGAVNLYH VREDGWIRVS SDNVADLHEK YSGSTP

UniProtKB: Proteasome subunit beta type-5

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Macromolecule #10: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 23.578986 KDa
SequenceString: RFSPYVFNGG TILAIAGEDF AIVASDTRLS EGFSIHTRDS PKCYKLTDKT VIGCSGFHGD CLTLTKIIEA RLKMYKHSNN KAMTTGAIA AMLSTILYSR RFFPYYVYNI IGGLDEEGKG AVYSFDPVGS YQRDSFKAGG SASAMLQPLL DNQVGFKNMQ N VEHVPLSL ...String:
RFSPYVFNGG TILAIAGEDF AIVASDTRLS EGFSIHTRDS PKCYKLTDKT VIGCSGFHGD CLTLTKIIEA RLKMYKHSNN KAMTTGAIA AMLSTILYSR RFFPYYVYNI IGGLDEEGKG AVYSFDPVGS YQRDSFKAGG SASAMLQPLL DNQVGFKNMQ N VEHVPLSL DRAMRLVKDV FISAAERDVY TGDALRICIV TKEGIREETV SLRKD

UniProtKB: Proteasome subunit beta type-1

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Macromolecule #11: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 24.41474 KDa
SequenceString: TQNPMVTGTS VLGVKFEGGV VIAADMLGSY GSLARFRNIS RIMRVNNSTM LGASGDYADF QYLKQVLGQM VIDEELLGDG HSYSPRAIH SWLTRAMYSR RSKMNPLWNT MVIGGYADGE SFLGYVDMLG VAYEAPSLAT GYGAYLAQPL LREVLEKQPV L SQTEARDL ...String:
TQNPMVTGTS VLGVKFEGGV VIAADMLGSY GSLARFRNIS RIMRVNNSTM LGASGDYADF QYLKQVLGQM VIDEELLGDG HSYSPRAIH SWLTRAMYSR RSKMNPLWNT MVIGGYADGE SFLGYVDMLG VAYEAPSLAT GYGAYLAQPL LREVLEKQPV L SQTEARDL VERCMRVLYY RDARSYNRFQ IATVTEKGVE IEGPLSTETN WDIAHMISGF E

UniProtKB: Proteasome subunit beta type-4

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Macromolecule #12: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 29.525842 KDa
SequenceString: MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGH AGTCLGILAN DGVLLAAERR NIHKLLDEVF FSEKIYKLNE DMACSVAGIT SDANVLTNE LRLIAQRYLL QYQEPIPCEQ LVTALCDIKQ AYTQFGGKRP FGVSLLYIGW DKHYGFQLYQ SDPSGNYGGW K ATCIGNNS ...String:
MSRRYDSRTT IFSPEGRLYQ VEYAMEAIGH AGTCLGILAN DGVLLAAERR NIHKLLDEVF FSEKIYKLNE DMACSVAGIT SDANVLTNE LRLIAQRYLL QYQEPIPCEQ LVTALCDIKQ AYTQFGGKRP FGVSLLYIGW DKHYGFQLYQ SDPSGNYGGW K ATCIGNNS AAAVSMLKQD YKEGEMTLKS ALALAIKVLN KTMDVSKLSA EKVEIATLTR ENGKTVIRVL KQKEVEQLIK KH EEEEAKA EREKKEKEQK EKDK

UniProtKB: Proteasome subunit alpha type-4

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Macromolecule #13: Isoform 3 of Proteasome subunit alpha-type 8

MacromoleculeName: Isoform 3 of Proteasome subunit alpha-type 8 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 27.886977 KDa
SequenceString: MASRYDRAIT VFSPDGHLFQ VEYAQEAVKK GSTAVGIRGT NIVVLGVEKK SVAKLQDERT VRKICALDDH VCMAFAGLTA DARVVINRA RVECQSHKLT VEDPVTVEYI TRFIATLKQK YTQSNGRRPF GISALIVGFD DDGISRLYQT DPSGTYHAWK A NAIGRSAK ...String:
MASRYDRAIT VFSPDGHLFQ VEYAQEAVKK GSTAVGIRGT NIVVLGVEKK SVAKLQDERT VRKICALDDH VCMAFAGLTA DARVVINRA RVECQSHKLT VEDPVTVEYI TRFIATLKQK YTQSNGRRPF GISALIVGFD DDGISRLYQT DPSGTYHAWK A NAIGRSAK TVREFLEKNY TEDAIASDSE AIKLAIKALL EVVQSGGKNI ELAIIRRNQP LKMFSAKEVE LYVTEIEKEK EE AEKKKSK KSV

UniProtKB: Proteasome subunit alpha-type 8

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Macromolecule #14: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 26.435977 KDa
SequenceString: MFLTRSEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI QTSEGVCLAV EKRITSPLME PSSIEKIVEI DAHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLFHMDPS G TFVQCDAR ...String:
MFLTRSEYDR GVNTFSPEGR LFQVEYAIEA IKLGSTAIGI QTSEGVCLAV EKRITSPLME PSSIEKIVEI DAHIGCAMSG LIADAKTLI DKARVETQNH WFTYNETMTV ESVTQAVSNL ALQFGEEDAD PGAMSRPFGV ALLFGGVDEK GPQLFHMDPS G TFVQCDAR AIGSASEGAQ SSLQEVYHKS MTLKEAIKSS LIILKQVMEE KLNATNIELA TVQPGQNFHM FTKEELEEVI KD I

UniProtKB: Proteasome subunit alpha type-5

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Macromolecule #15: Proteasome activator complex subunit 4

MacromoleculeName: Proteasome activator complex subunit 4 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human) / Tissue: testis
Molecular weightTheoretical: 211.593344 KDa
SequenceString: MEPAERAGVG EPPEPGGRPE PGPRGFVPQK EIVYNKLLPY AERLDAESDL QLAQIKCNLG RAVQLQELWP GGLFWTRKLS TYIRLYGRK FSKEDHVLFI KLLYELVSIP KLEISMMQGF ARLLINLLKK KELLSRADLE LPWRPLYDMV ERILYSKTEH L GLNWFPNS ...String:
MEPAERAGVG EPPEPGGRPE PGPRGFVPQK EIVYNKLLPY AERLDAESDL QLAQIKCNLG RAVQLQELWP GGLFWTRKLS TYIRLYGRK FSKEDHVLFI KLLYELVSIP KLEISMMQGF ARLLINLLKK KELLSRADLE LPWRPLYDMV ERILYSKTEH L GLNWFPNS VENILKTLVK SCRPYFPADA TAEMLEEWRP LMCPFDVTMQ KAITYFEIFL PTSLPPELHH KGFKLWFDEL IG LWVSVQN LPQWEGQLVN LFARLATDNI GYIDWDPYVP KIFTRILRSL NLPVGSSQVL VPRFLTNAYD IGHAVIWITA MMG GPSKLV QKHLAGLFNS ITSFYHPSNN GRWLNKLMKL LQRLPNSVVR RLHRERYKKP SWLTPVPDSH KLTDQDVTDF VQCI IQPVL LAMFSKTGSL EAAQALQNLA LMRPELVIPP VLERTYPALE TLTEPHQLTA TLSCVIGVAR SLVSGGRWFP EGPTH MLPL LMRALPGVDP NDFSKCMITF QFIATFSTLV PLVDCSSVLQ ERNDLTEVER ELCSATAEFE DFVLQFMDRC FGLIES STL EQTREETETE KMTHLESLVE LGLSSTFSTI LTQCSKEIFM VALQKVFNFS TSHIFETRVA GRMVADMCRA AVKCCPE ES LKLFVPHCCS VITQLTMNDD VLNDEELDKE LLWNLQLLSE ITRVDGRKLL LYREQLVKIL QRTLHLTCKQ GYTLSCNL L HHLLRSTTLI YPTEYCSVPG GFDKPPSEYF PIKDWGKPGD LWNLGIQWHV PSSEEVSFAF YLLDSFLQPE LVKLQHCGD GKLEMSRDDI LQSLTIVHNC LIGSGNLLPP LKGEPVTNLV PSMVSLEETK LYTGLEYDLS RENHREVIAT VIRKLLNHIL DNSEDDTKS LFLIIKIIGD LLQFQGSHKH EFDSRWKSFN LVKKSMENRL HGKKQHIRAL LIDRVMLQHE LRTLTVEGCE Y KKIHQDMI RDLLRLSTSS YSQVRNKAQQ TFFAALGAYN FCCRDIIPLV LEFLRPDRQG VTQQQFKGAL YCLLGNHSGV CL ANLHDWD CIVQTWPAIV SSGLSQAMSL EKPSIVRLFD DLAEKIHRQY ETIGLDFTIP KSCVEIAELL QQSKNPSINQ ILL SPEKIK EGIKRQQEKN ADALRNYENL VDTLLDGVEQ RNLPWKFEHI GIGLLSLLLR DDRVLPLRAI RFFVENLNHD AIVV RKMAI SAVAGILKQL KRTHKKLTIN PCEISGCPKP TQIIAGDRPD NHWLHYDSKT IPRTKKEWES SCFVEKTHWG YYTWP KNMV VYAGVEEQPK LGRSREDMTE AEQIIFDHFS DPKFVEQLIT FLSLEDRKGK DKFNPRRFCL FKGIFRNFDD AFLPVL KPH LEHLVADSHE STQRCVAEII AGLIRGSKHW TFEKVEKLWE LLCPLLRTAL SNITVETYND WGACIATSCE SRDPRKL HW LFELLLESPL SGEGGSFVDA CRLYVLQGGL AQQEWRVPEL LHRLLKYLEP KLTQVYKNVR ERIGSVLTYI FMIDVSLP N TTPTISPHVP EFTARILEKL KPLMDVDEEI QNHVMEENGI GEEDERTQGI KLLKTILKWL MASAGRSFST AVTEQLQLL PLFFKIAPVE NDNSYDELKR DAKLCLSLMS QGLLYPHQVP LVLQVLKQTA RSSSWHARYT VLTYLQTMVF YNLFIFLNNE DAVKDIRWL VISLLEDEQL EVREMAATTL SGLLQCNFLT MDSPMQIHFE QLCKTKLPKK RKRDPGSVGD TIPSAELVKR H AGVLGLGA CVLSSPYDVP TWMPQLLMNL SAHLNDPQPI EMTVKKTLSN FRRTHHDNWQ EHKQQFTDDQ LLVLTDLLVS PC YYA

UniProtKB: Proteasome activator complex subunit 4

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Macromolecule #16: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 16 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
25.0 mMHEPES
5.0 mMmagnesium chlorideMgCl2
100.0 mMsodium chlorideNaCl
1.0 mMDTT
1.0 mMATP

Details: 25 mM HEPES pH 7.4, 100 mM NaCl, 1 mM ATP, 1 mM DTT, 5 mM MgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average exposure time: 3.0 sec. / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
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

Particle selectionNumber selected: 896000
CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: Ab-initio reconstruction, cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4.1) / Number images used: 6748
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.4.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6kwy


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 74 / Target criteria: cross-correlation coefficient
Output model

PDB-9tms:
Human sperm 20S-PA200 proteasome complex isolated from native source

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