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- EMDB-53264: Ternary complex of the human 20S proteasome in complex with Impor... -

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Basic information

Entry
Database: EMDB / ID: EMD-53264
TitleTernary complex of the human 20S proteasome in complex with Importin-9 and two homodimers of Akirin-2 - focussed refinement on the alpha subunits, Ipo-9 and Ak2
Map data
Sample
  • Complex: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9
    • Protein or peptide: Akirin-2
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit alpha type-6
    • 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: Importin-9
Keywords20S proteasome / 20S / proteasome / nuclear iport / akirin / akirin2 / importin 9 / importin / PROTEIN TRANSPORT
Function / homology
Function and homology information


proteasome localization / regulation of muscle cell differentiation / positive regulation of B cell activation / histone chaperone activity / nuclear protein quality control by the ubiquitin-proteasome system / positive regulation of adaptive immune response / purine ribonucleoside triphosphate binding / embryo development ending in birth or egg hatching / sperm glycocalyx / Antigen processing: Ub, ATP-independent proteasomal degradation ...proteasome localization / regulation of muscle cell differentiation / positive regulation of B cell activation / histone chaperone activity / nuclear protein quality control by the ubiquitin-proteasome system / positive regulation of adaptive immune response / purine ribonucleoside triphosphate binding / embryo development ending in birth or egg hatching / sperm glycocalyx / Antigen processing: Ub, ATP-independent proteasomal degradation / perinuclear theca / positive regulation of innate immune response / Regulation of ornithine decarboxylase (ODC) / nuclear import signal receptor activity / Proteasome assembly / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / sperm head-tail coupling apparatus / myofibril / immune system process / NF-kappaB binding / proteasome core complex, alpha-subunit complex / transcription repressor complex / ciliary tip / proteasome complex / : / sarcomere / sperm end piece / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / transcription coregulator activity / Asymmetric localization of PCP proteins / centriole / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / negative regulation of inflammatory response to antigenic stimulus / Assembly of the pre-replicative complex / P-body / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / lipopolysaccharide binding / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Hedgehog ligand biogenesis / Degradation of GLI1 by the proteasome / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / 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 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of CDH1 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / cerebral cortex development / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / positive regulation of interleukin-6 production / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / response to virus / FCERI mediated NF-kB activation / small GTPase binding / Regulation of expression of SLITs and ROBOs / nuclear matrix / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / protein import into nucleus / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / KEAP1-NFE2L2 pathway / UCH proteinases / Downstream TCR signaling / nuclear envelope / sperm principal piece / Antigen processing: Ubiquitination & Proteasome degradation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / Neddylation / sperm midpiece
Similarity search - Function
: / Importin-11-like, TPR repeats / : / Importin-9 central HEAT repeats / Akirin / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Proteasome subunit alpha 1 ...: / Importin-11-like, TPR repeats / : / Importin-9 central HEAT repeats / Akirin / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Proteasome subunit alpha 1 / Proteasome subunit alpha5 / Proteasome subunit alpha6 / 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 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 alpha type-7 / 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 alpha type-6 / Akirin-2 / Importin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsBrunner HL / Grundmann L / David H
Funding supportEuropean Union, Austria, 2 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission847548European Union
Austrian Science Fund10.55776/F79 Austria
CitationJournal: Nat Commun / Year: 2026
Title: A multivalent adaptor mechanism drives the nuclear import of proteasomes.
Authors: Hanna L Brunner / Robert W Kalis / Lorenz Grundmann / Zuzana Hodáková / Zuzana Koskova / Irina Grishkovskaya / Melanie de Almeida / Matthias Hinterndorfer / Hannah Knaudt / Simon Höfflin ...Authors: Hanna L Brunner / Robert W Kalis / Lorenz Grundmann / Zuzana Hodáková / Zuzana Koskova / Irina Grishkovskaya / Melanie de Almeida / Matthias Hinterndorfer / Hannah Knaudt / Simon Höfflin / Florian Andersch / Harald Kotisch / Achim Dickmanns / Sara Cuylen-Haering / Johannes Zuber / David Haselbach /
Abstract: Nuclear protein homeostasis, including transcription factor turnover, critically depends on the nuclear proteasomes that must be imported after cell division. This dynamic process requires AKIRIN2, a ...Nuclear protein homeostasis, including transcription factor turnover, critically depends on the nuclear proteasomes that must be imported after cell division. This dynamic process requires AKIRIN2, a small unstructured protein whose mechanistic role has remained elusive despite its essential function. Using an integrated approach combining protein-wide saturation mutagenesis screens, cryo-EM, and biochemical reconstitution, we characterize AKIRIN2 as a scaffold protein that coordinates the assembly of an importin cluster around the proteasome. AKIRIN2 binds in multiple copies to the 20S proteasome and simultaneously interacts with importin IPO9 and the KPNA2/KPNB1 heterodimer. In the nucleus, RanGTP triggers importin dissociation, releasing the proteasome, while AKIRIN2 undergoes ubiquitin-independent degradation. Our findings reveal how AKIRIN2's multivalency facilitates the recruitment of multiple importins to the proteasome, a critical adaptation for transporting this large macromolecular complex into the nucleus and maintaining the nuclear proteome.
History
DepositionMar 26, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53264.png

Downloads & links

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Map

FileDownload / File: emd_53264.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 300 pix.
= 429. Å		1.43 Å/pix.
x 300 pix.
= 429. Å		1.43 Å/pix.
x 300 pix.
= 429. Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
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Contour LevelBy AUTHOR: 0.0313
Minimum - Maximum-0.013655666 - 1.8800604
Average (Standard dev.)0.0010453782 (±0.022466542)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 428.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53264_msk_1.map
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Additional map: #1

Fileemd_53264_additional_1.map
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Half map: #2

Fileemd_53264_half_map_1.map
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Half map: #1

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Sample components

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Entire : Ternary complex of the human 20S proteasome in complex with two d...

EntireName: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9
Components
  • Complex: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9
    • Protein or peptide: Akirin-2
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit alpha type-6
    • 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: Importin-9

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Supramolecule #1: Ternary complex of the human 20S proteasome in complex with two d...

SupramoleculeName: Ternary complex of the human 20S proteasome in complex with two dimers of Akirin-2 and Importin-9
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#9, #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Importin-9

MacromoleculeName: Importin-9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 116.06232 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MAAAAAAGAA SGLPGPVAQG LKEALVDTLT GILSPVQEVR AAAEEQIKVL EVTEEFGVHL AELTVDPQGA LAIRQLASVI LKQYVETHW CAQSEKFRPP ETTERAKIVI RELLPNGLRE SISKVRSSVA YAVSAIAHWD WPEAWPQLFN LLMEMLVSGD L NAVHGAMR ...String:
MAAAAAAGAA SGLPGPVAQG LKEALVDTLT GILSPVQEVR AAAEEQIKVL EVTEEFGVHL AELTVDPQGA LAIRQLASVI LKQYVETHW CAQSEKFRPP ETTERAKIVI RELLPNGLRE SISKVRSSVA YAVSAIAHWD WPEAWPQLFN LLMEMLVSGD L NAVHGAMR VLTEFTREVT DTQMPLVAPV ILPEMYKIFT MAEVYGIRTR SRAVEIFTTC AHMICNMEEL EKGAAKVLIF PV VQQFTEA FVQALQIPDG PTSDSGFKME VLKAVTALVK NFPKHMVSSM QQILPIVWNT LTESAAFYVR TEVNYTEEVE DPV DSDGEV LGFENLVFSI FEFVHALLEN SKFKSTVKKA LPELIYYIIL YMQITEEQIK VWTANPQQFV EDEDDDTFSY TVRI AAQDL LLAVATDFQN ESAAALAAAA TRHLQEAEQT KNSGTEHWWK IHEACMLALG SVKAIITDSV KNGRIHFDMH GFLTN VILA DLNLSVSPFL LGRALWAASR FTVAMSPELI QQFLQATVSG LHETQPPSVR ISAVRAIWGY CDQLKVSEST HVLQPF LPS ILDGLIHLAA QFSSEVLNLV METLCIVCTV DPEFTASMES KICPFTIAIF LKYSNDPVVA SLAQDIFKEL SQIEACQ GP MQMRLIPTLV SIMQAPADKI PAGLCATAID ILTTVVRNTK PPLSQLLICQ AFPAVAQCTL HTDDNATMQN GGECLRAY V SVTLEQVAQW HDEQGHNGLW YVMQVVSQLL DPRTSEFTAA FVGRLVSTLI SKAGRELGEN LDQILRAILS KMQQAETLS VMQSLIMVFA HLVHTQLEPL LEFLCSLPGP TGKPALEFVM AEWTSRQHLF YGQYEGKVSS VALCKLLQHG INADDKRLQD IRVKGEEIY SMDEGIRTRS KSAKNPERWT NIPLLVKILK LIINELSNVM EANAARQATP AEWSQDDSND MWEDQEEEEE E EEDGLAGQ LLSDILATSK YEEDYYEDDE EDDPDALKDP LYQIDLQAYL TDFLCQFAQQ PCYIMFSGHL NDNERRVLQT IG I

UniProtKB: Importin-9

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Macromolecule #2: Akirin-2

MacromoleculeName: Akirin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.525582 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (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 #3: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.469252 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #4: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.432459 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #5: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.927535 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #6: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.525842 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #7: Proteasome subunit alpha type-7

MacromoleculeName: Proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.929891 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #8: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.435977 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 #9: Proteasome subunit alpha type-1

MacromoleculeName: Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.595627 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
GridModel: Quantifoil R3.5/1 / Support film - #0 - Film type ID: 1 / Support film - #0 - Material: CARBON / Support film - #0 - topology: HOLEY / Support film - #1 - Film type ID: 2 / Support film - #1 - Material: CARBON / Support film - #1 - topology: CONTINUOUS / Support film - #1 - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 44.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 61740
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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