EMDB-11649: Akirin2 bound to the human 26S proteasome

Basic information

• Entry: Database: EMDB / ID: EMD-11649
• Title: Akirin2 bound to the human 26S proteasome

Sample

• Complex: Akirin2 bound to the human 26S proteasome

Function / homology

Function:

proteasome localization / regulation of muscle cell differentiation / positive regulation of B cell activation / 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 / positive regulation of innate immune response / 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 / transcription coregulator activity / TNFR2 non-canonical NF-kB pathway / 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 / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / lipopolysaccharide binding / Degradation of AXIN / negative regulation of inflammatory response to antigenic stimulus / Hh mutants are degraded by ERAD / 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 / Regulation of RUNX3 expression and activity / Vif-mediated degradation of APOBEC3G / 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 / 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 / response to virus / FCERI mediated NF-kB activation / Regulation of expression of SLITs and ROBOs / Regulation of PTEN stability and activity / nuclear matrix / 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 / Antigen processing: Ubiquitination & Proteasome degradation / peptidase activity / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / response to oxidative stress / regulation of inflammatory response / secretory granule lumen / protein-macromolecule adaptor activity / response to lipopolysaccharide / endopeptidase activity / adaptive immune response / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction

Domain/homology:

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 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

Component:

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

• Biological species: Homo sapiens (human)
• Method: single particle reconstruction / negative staining / Resolution: 21.0 Å
• Authors: De Almeida MT / Hinterndorfer M / Grishkovskaya I / Haselbach D / Zuber J
• 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 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 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

Deposition	Aug 21, 2020	-
Header (metadata) release	Sep 1, 2021	-
Map release	Sep 1, 2021	-
Update	Dec 1, 2021	-
Current status	Dec 1, 2021	Processing site: PDBe / Status: Released

Map

• File: Download / File: emd_11649.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.85 Å

Density

Contour Level	By AUTHOR: 0.0029 / Movie #1: 0.0029
Minimum - Maximum	-0.042500027 - 0.041203734
Average (Standard dev.)	-3.4781406e-05 (±0.0025890071)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 300 300 300 Spacing 300 300 300
Cell	A=B=C: 555.0 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.85	1.85	1.85
M x/y/z	300	300	300
origin x/y/z	0.000	0.000	0.000
length x/y/z	555.000	555.000	555.000
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	300	300	300
D min/max/mean	-0.043	0.041	-0.000

Supplemental data

Sample components

Entire : Akirin2 bound to the human 26S proteasome

• Entire: Name: Akirin2 bound to the human 26S proteasome

Components

• Complex: Akirin2 bound to the human 26S proteasome

Supramolecule #1: Akirin2 bound to the human 26S proteasome

• Supramolecule: Name: Akirin2 bound to the human 26S proteasome / type: complex / ID: 1 / Parent: 0
• Source (natural): Organism: Homo sapiens (human)
• Recombinant expression: Organism: Escherichia coli (E. coli)

Experimental details

Structure determination

• Method: negative staining
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Buffer: pH: 6.5
• Staining: Type: NEGATIVE / Material: Uranyl Acetate
• Grid: Model: Homemade / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR

Electron microscopy

• Microscope: FEI TECNAI 20
• Image recording: Film or detector model: FEI EAGLE (2k x 2k) / Average electron dose: 60.0 e/Ų
• Electron beam: Acceleration voltage: 200 kV / Electron source: LAB6
• Electron optics: C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm

Image processing

• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 36000
• Initial angle assignment: Type: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1)
• Final angle assignment: Type: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
• Final 3D classification: Number classes: 5 / Avg.num./class: 25000 / Software - Name: RELION (ver. 3.1)