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- EMDB-12341: Akirin2 bound human proteasome -

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Basic information

Entry
Database: EMDB / ID: EMD-12341
TitleAkirin2 bound human proteasome
Map datadenoised map
Sample
  • Complex: Akirin2 bound to 20S proteasome
    • Complex: 20S proteasome
      • Protein or peptide: x 14 types
    • Complex: Akirin2
      • Protein or peptide: x 1 types
  • Ligand: x 1 types
Keywordsproteasome / nuclear import / TRANSPORT PROTEIN
Function / homology
Function and homology information


proteasome localization / regulation of muscle cell differentiation / positive regulation of B cell activation / positive regulation of adaptive immune response / nuclear protein quality control by the ubiquitin-proteasome system / purine ribonucleoside triphosphate binding / positive regulation of innate immune response / embryo development ending in birth or egg hatching / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly ...proteasome localization / regulation of muscle cell differentiation / positive regulation of B cell activation / positive regulation of adaptive immune response / nuclear protein quality control by the ubiquitin-proteasome system / purine ribonucleoside triphosphate binding / positive regulation of innate immune response / embryo development ending in birth or egg hatching / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / proteasome core complex / Somitogenesis / myofibril / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / transcription repressor complex / proteasome complex / proteolysis involved in protein catabolic process / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / transcription coregulator activity / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / lipopolysaccharide binding / Degradation of AXIN / Hh mutants are degraded by ERAD / negative regulation of inflammatory response to antigenic stimulus / P-body / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / : / Degradation of beta-catenin by the destruction complex / cerebral cortex development / response to virus / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / CDK-mediated phosphorylation and removal of Cdc6 / positive regulation of interleukin-6 production / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / protein import into nucleus / Regulation of RAS by GAPs / positive regulation of NF-kappaB transcription factor activity / Regulation of RUNX2 expression and activity / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / peptidase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / regulation of inflammatory response / protein-macromolecule adaptor activity / secretory granule lumen / endopeptidase activity / adaptive immune response / response to oxidative stress / response to lipopolysaccharide / proteasome-mediated ubiquitin-dependent protein catabolic process
Similarity search - Function
Akirin / 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 alpha6 / Proteasome subunit alpha5 / Proteasome beta-type subunits signature. ...Akirin / 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 alpha6 / Proteasome subunit alpha5 / 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 alpha type-7 / 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 alpha type-7 / 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 / Akirin-2 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsSingh K / Brunner H / Grishkovskaya I / de Almeida M / Hinterndorfer M / Zuber J / Haselbach D
CitationJournal: Nature / Year: 2021
Title: AKIRIN2 controls the nuclear import of proteasomes in vertebrates.
Authors: Melanie de Almeida / Matthias Hinterndorfer / Hanna Brunner / Irina Grishkovskaya / Kashish Singh / Alexander Schleiffer / Julian Jude / Sumit Deswal / Robert Kalis / Milica Vunjak / Thomas ...Authors: Melanie de Almeida / Matthias Hinterndorfer / Hanna Brunner / Irina Grishkovskaya / Kashish Singh / Alexander Schleiffer / Julian Jude / Sumit Deswal / Robert Kalis / Milica Vunjak / Thomas Lendl / Richard Imre / Elisabeth Roitinger / Tobias Neumann / Susanne Kandolf / Michael Schutzbier / Karl Mechtler / Gijs A Versteeg / David Haselbach / Johannes Zuber /
Abstract: Protein expression and turnover are controlled through a complex interplay of transcriptional, post-transcriptional and post-translational mechanisms to enable spatial and temporal regulation of ...Protein expression and turnover are controlled through a complex interplay of transcriptional, post-transcriptional and post-translational mechanisms to enable spatial and temporal regulation of cellular processes. To systematically elucidate such gene regulatory networks, we developed a CRISPR screening assay based on time-controlled Cas9 mutagenesis, intracellular immunostaining and fluorescence-activated cell sorting that enables the identification of regulatory factors independent of their effects on cellular fitness. We pioneered this approach by systematically probing the regulation of the transcription factor MYC, a master regulator of cell growth. Our screens uncover a highly conserved protein, AKIRIN2, that is essentially required for nuclear protein degradation. We found that AKIRIN2 forms homodimers that directly bind to fully assembled 20S proteasomes to mediate their nuclear import. During mitosis, proteasomes are excluded from condensing chromatin and re-imported into newly formed daughter nuclei in a highly dynamic, AKIRIN2-dependent process. Cells undergoing mitosis in the absence of AKIRIN2 become devoid of nuclear proteasomes, rapidly causing accumulation of MYC and other nuclear proteins. Collectively, our study reveals a dedicated pathway controlling the nuclear import of proteasomes in vertebrates and establishes a scalable approach to decipher regulators in essential cellular processes.
History
DepositionFeb 11, 2021-
Header (metadata) releaseSep 1, 2021-
Map releaseSep 1, 2021-
UpdateJul 10, 2024-
Current statusJul 10, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nht
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7nht
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12341.png

Downloads & links

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Map

FileDownload / File: emd_12341.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationdenoised map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å		1.06 Å/pix.
x 360 pix.
= 381.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.016 / Movie #1: 0.07
Minimum - Maximum-0.016013445 - 1.7188772
Average (Standard dev.)0.0016291521 (±0.030343458)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 381.59998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z381.600381.600381.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0161.7190.002

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Supplemental data

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Additional map: unsharpend map

Fileemd_12341_additional_1.map
Annotationunsharpend map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Akirin2 bound to 20S proteasome

EntireName: Akirin2 bound to 20S proteasome
Components
  • Complex: Akirin2 bound to 20S proteasome
    • Complex: 20S proteasome
      • Protein or peptide: Proteasome subunit alpha type-2
      • Protein or peptide: Proteasome subunit alpha type-4
      • Protein or peptide: Proteasome subunit alpha type-7
      • Protein or peptide: Proteasome subunit alpha type-5
      • Protein or peptide: Proteasome subunit alpha type-1
      • Protein or peptide: Proteasome subunit alpha type-3
      • Protein or peptide: Proteasome subunit alpha 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 beta type-6
    • Complex: Akirin2
      • Protein or peptide: Akirin-2
  • Ligand: POTASSIUM ION

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Supramolecule #1: Akirin2 bound to 20S proteasome

SupramoleculeName: Akirin2 bound to 20S proteasome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#15
Molecular weightTheoretical: 780 KDa

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Supramolecule #2: 20S proteasome

SupramoleculeName: 20S proteasome / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#14
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Akirin2

SupramoleculeName: Akirin2 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #15
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #2: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #3: Proteasome subunit alpha type-7

MacromoleculeName: Proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.929891 KDa
SequenceString: MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGRDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAGLTADA RIVINRARV ECQSHRLTVE DPVTVEYITR YIASLKQRYT QSNGRRPFGI SALIVGFDFD GTPRLYQTDP SGTYHAWKAN A IGRGAKSV ...String:
MSYDRAITVF SPDGHLFQVE YAQEAVKKGS TAVGVRGRDI VVLGVEKKSV AKLQDERTVR KICALDDNVC MAFAGLTADA RIVINRARV ECQSHRLTVE DPVTVEYITR YIASLKQRYT QSNGRRPFGI SALIVGFDFD GTPRLYQTDP SGTYHAWKAN A IGRGAKSV REFLEKNYTD EAIETDDLTI KLVIKALLEV VQSGGKNIEL AVMRRDQSLK ILNPEEIEKY VAEIEKEKEE NE KKKQKKA S

UniProtKB: Proteasome subunit alpha type-7

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Macromolecule #4: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #5: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #6: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #7: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #8: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.000418 KDa
SequenceString: MAAVSVYAPP VGGFSFDNCR RNAVLEADFA KRGYKLPKVR KTGTTIAGVV YKDGIVLGAD TRATEGMVVA DKNCSKIHFI SPNIYCCGA GTAADTDMTT QLISSNLELH SLSTGRLPRV VTANRMLKQM LFRYQGYIGA ALVLGGVDVT GPHLYSIYPH G STDKLPYV ...String:
MAAVSVYAPP VGGFSFDNCR RNAVLEADFA KRGYKLPKVR KTGTTIAGVV YKDGIVLGAD TRATEGMVVA DKNCSKIHFI SPNIYCCGA GTAADTDMTT QLISSNLELH SLSTGRLPRV VTANRMLKQM LFRYQGYIGA ALVLGGVDVT GPHLYSIYPH G STDKLPYV TMGSGSLAAM AVFEDKFRPD MEEEEAKNLV SEAIAAGIFN DLGSGSNIDL CVISKNKLDF LRPYTVPNKK GT RLGRYRC EKGTTAVLTE KITPLEIEVL EETVQTMDTS

UniProtKB: Proteasome subunit beta type-7

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Macromolecule #9: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
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 #10: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
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 #11: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.510248 KDa
SequenceString: MALASVLERP LPVNQRGFFG LGGRADLLDL GPGSLSDGLS LAAPGWGVPE EPGIEMLHGT TTLAFKFRHG VIVAADSRAT AGAYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQY KGMGLSMGTM I CGWDKRGP ...String:
MALASVLERP LPVNQRGFFG LGGRADLLDL GPGSLSDGLS LAAPGWGVPE EPGIEMLHGT TTLAFKFRHG VIVAADSRAT AGAYIASQT VKKVIEINPY LLGTMAGGAA DCSFWERLLA RQCRIYELRN KERISVAAAS KLLANMVYQY KGMGLSMGTM I CGWDKRGP GLYYVDSEGN RISGATFSVG SGSVYAYGVM DRGYSYDLEV EQAYDLARRA IYQATYRDAY SGGAVNLYHV RE DGWIRVS SDNVADLHEK YSGSTP

UniProtKB: Proteasome subunit beta type-5

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Macromolecule #12: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.522396 KDa
SequenceString: MLSSTAMYSA PGRDLGMEPH RAAGPLQLRF SPYVFNGGTI LAIAGEDFAI VASDTRLSEG FSIHTRDSPK CYKLTDKTVI GCSGFHGDC LTLTKIIEAR LKMYKHSNNK AMTTGAIAAM LSTILYSRRF FPYYVYNIIG GLDEEGKGAV YSFDPVGSYQ R DSFKAGGS ...String:
MLSSTAMYSA PGRDLGMEPH RAAGPLQLRF SPYVFNGGTI LAIAGEDFAI VASDTRLSEG FSIHTRDSPK CYKLTDKTVI GCSGFHGDC LTLTKIIEAR LKMYKHSNNK AMTTGAIAAM LSTILYSRRF FPYYVYNIIG GLDEEGKGAV YSFDPVGSYQ R DSFKAGGS ASAMLQPLLD NQVGFKNMQN VEHVPLSLDR AMRLVKDVFI SAAERDVYTG DALRICIVTK EGIREETVSL RK D

UniProtKB: Proteasome subunit beta type-1

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Macromolecule #13: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.231178 KDa
SequenceString: MEAFLGSRSG LWAGGPAPGQ FYRIPSTPDS FMDPASALYR GPITRTQNPM VTGTSVLGVK FEGGVVIAAD MLGSYGSLAR FRNISRIMR VNNSTMLGAS GDYADFQYLK QVLGQMVIDE ELLGDGHSYS PRAIHSWLTR AMYSRRSKMN PLWNTMVIGG Y ADGESFLG ...String:
MEAFLGSRSG LWAGGPAPGQ FYRIPSTPDS FMDPASALYR GPITRTQNPM VTGTSVLGVK FEGGVVIAAD MLGSYGSLAR FRNISRIMR VNNSTMLGAS GDYADFQYLK QVLGQMVIDE ELLGDGHSYS PRAIHSWLTR AMYSRRSKMN PLWNTMVIGG Y ADGESFLG YVDMLGVAYE APSLATGYGA YLAQPLLREV LEKQPVLSQT EARDLVERCM RVLYYRDARS YNRFQIATVT EK GVEIEGP LSTETNWDIA HMISGFE

UniProtKB: Proteasome subunit beta type-4

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Macromolecule #14: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.377652 KDa
SequenceString: MAATLLAARG AGPAPAWGPE AFTPDWESRE VSTGTTIMAV QFDGGVVLGA DSRTTTGSYI ANRVTDKLTP IHDRIFCCRS GSAADTQAV ADAVTYQLGF HSIELNEPPL VHTAASLFKE MCYRYREDLM AGIIIAGWDP QEGGQVYSVP MGGMMVRQSF A IGGSGSSY ...String:
MAATLLAARG AGPAPAWGPE AFTPDWESRE VSTGTTIMAV QFDGGVVLGA DSRTTTGSYI ANRVTDKLTP IHDRIFCCRS GSAADTQAV ADAVTYQLGF HSIELNEPPL VHTAASLFKE MCYRYREDLM AGIIIAGWDP QEGGQVYSVP MGGMMVRQSF A IGGSGSSY IYGYVDATYR EGMTKEECLQ FTANALALAM ERDGSSGGVI RLAAIAESGV ERQVLLGDQI PKFAVATLPP A

UniProtKB: Proteasome subunit beta type-6

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Macromolecule #15: Akirin-2

MacromoleculeName: Akirin-2 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.525582 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MACGATLKRT LDFDPLLSPA SPKRRRCAPL SAPTSAAASP LSAAAATAAS FSAAAASPQK YLRMEPSPFG DVSSRLTTEQ ILYNIKQEY KRMQKRRHLE TSFQQTDPCC TSDAQPHAFL LSGPASPGTS SAASSPLKKE QPLFTLRQVG MICERLLKER E EKVREEYE ...String:
MACGATLKRT LDFDPLLSPA SPKRRRCAPL SAPTSAAASP LSAAAATAAS FSAAAASPQK YLRMEPSPFG DVSSRLTTEQ ILYNIKQEY KRMQKRRHLE TSFQQTDPCC TSDAQPHAFL LSGPASPGTS SAASSPLKKE QPLFTLRQVG MICERLLKER E EKVREEYE EILNTKLAEQ YDAFVKFTHD QIMRRYGEQP ASYVS

UniProtKB: Akirin-2

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Macromolecule #16: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 16 / Number of copies: 3 / Formula: K
Molecular weightTheoretical: 39.098 Da

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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

BufferpH: 6.5
Component:
ConcentrationNameFormula
50.0 mMBisTris
50.0 mMpotassium chlorideKCl
5.0 mMmagnesium chlorideMgCl2
2.0 mMDithiothreitolDTT
2.0 mMAdenosin triphosphateATP
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4595 / Average exposure time: 1.0 sec. / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 81000
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: 1427356
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 37447
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

Initial modelPDB ID:

5le5


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: RECIPROCAL / Protocol: FLEXIBLE FIT
Output model

PDB-7nht:
Akirin2 bound human proteasome

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