+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12341 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Akirin2 bound human proteasome | |||||||||
Map data | denoised map | |||||||||
Sample |
| |||||||||
Keywords | proteasome / nuclear import / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information positive regulation of endopeptidase activity / purine ribonucleoside triphosphate binding / positive regulation of innate immune response / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / embryo development ending in birth or egg hatching / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process ...positive regulation of endopeptidase activity / purine ribonucleoside triphosphate binding / positive regulation of innate immune response / regulation of endopeptidase activity / Regulation of ornithine decarboxylase (ODC) / embryo development ending in birth or egg hatching / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / immune system process / myofibril / : / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / transcription repressor complex / sarcomere / proteasome complex / ciliary basal body / Regulation of activated PAK-2p34 by proteasome mediated degradation / proteolysis involved in protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Asymmetric localization of PCP proteins / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / lipopolysaccharide binding / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / transcription coregulator activity / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / P-body / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / 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 / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / response to virus / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / response to organic cyclic compound / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / positive regulation of interleukin-6 production / Regulation of expression of SLITs and ROBOs / nuclear matrix / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / positive regulation of NF-kappaB transcription factor activity / peptidase activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / ER-Phagosome pathway / regulation of inflammatory response / secretory granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / response to oxidative stress / ficolin-1-rich granule lumen / postsynapse / response to lipopolysaccharide / nuclear body / Ub-specific processing proteases / ribosome / cadherin binding / negative regulation of gene expression Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Singh K / Brunner H / Grishkovskaya I / de Almeida M / Hinterndorfer M / Zuber J / Haselbach D | |||||||||
Citation | Journal: 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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_12341.map.gz | 150.9 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-12341-v30.xml emd-12341.xml | 35 KB 35 KB | Display Display | EMDB header |
Images | emd_12341.png | 72.5 KB | ||
Filedesc metadata | emd-12341.cif.gz | 9.1 KB | ||
Others | emd_12341_additional_1.map.gz | 141.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12341 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12341 | HTTPS FTP |
-Validation report
Summary document | emd_12341_validation.pdf.gz | 359 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_12341_full_validation.pdf.gz | 358.5 KB | Display | |
Data in XML | emd_12341_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_12341_validation.cif.gz | 8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12341 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12341 | HTTPS FTP |
-Related structure data
Related structure data | 7nhtMC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data | |
EM raw data | EMPIAR-10752 (Title: Single particle cryo EM Data of a human Akirin2 proteasome complex Data size: 2.0 TB Data #1: Unaligned Multiframe micrographs of Akirin2 bound to the human proteasome [micrographs - multiframe] Data #2: Motion corrected files dose weighted and summed as well as without dose weigthening [micrographs - single frame] Data #3: Extracted particles of an Akirin2 bound proteasome [picked particles - single frame - processed]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_12341.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | denoised map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Additional map: unsharpend map
File | emd_12341_additional_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | unsharpend map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
+Entire : Akirin2 bound to 20S proteasome
+Supramolecule #1: Akirin2 bound to 20S proteasome
+Supramolecule #2: 20S proteasome
+Supramolecule #3: Akirin2
+Macromolecule #1: Proteasome subunit alpha type-2
+Macromolecule #2: Proteasome subunit alpha type-4
+Macromolecule #3: Proteasome subunit alpha type-7
+Macromolecule #4: Proteasome subunit alpha type-5
+Macromolecule #5: Proteasome subunit alpha type-1
+Macromolecule #6: Proteasome subunit alpha type-3
+Macromolecule #7: Proteasome subunit alpha type-6
+Macromolecule #8: Proteasome subunit beta type-7
+Macromolecule #9: Proteasome subunit beta type-3
+Macromolecule #10: Proteasome subunit beta type-2
+Macromolecule #11: Proteasome subunit beta type-5
+Macromolecule #12: Proteasome subunit beta type-1
+Macromolecule #13: Proteasome subunit beta type-4
+Macromolecule #14: Proteasome subunit beta type-6
+Macromolecule #15: Akirin-2
+Macromolecule #16: POTASSIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 Component:
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Grid | Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 81000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |