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:

positive regulation of endopeptidase activity / purine ribonucleoside triphosphate binding / positive regulation of innate immune response / regulation of endopeptidase activity / proteasome core complex / embryo development ending in birth or egg hatching / Regulation of ornithine decarboxylase (ODC) / 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 / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / proteolysis involved in protein catabolic process / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / 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 / Hh mutants are degraded by ERAD / lipopolysaccharide binding / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / 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 / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / 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 / P-body / 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 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / 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 / 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 / positive regulation of interleukin-6 production / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / peptidase activity / positive regulation of NF-kappaB transcription factor activity / ER-Phagosome pathway / regulation of inflammatory response / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / endopeptidase activity / response to oxidative stress / ficolin-1-rich granule lumen / response to lipopolysaccharide / nuclear body / ribosome / Ub-specific processing proteases / cadherin binding / negative regulation of gene expression

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 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 alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-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)