7NHT

Akirin2 bound human proteasome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

AKIRIN2 controls the nuclear import of proteasomes in vertebrates.

de Almeida, M.Hinterndorfer, M.Brunner, H.Grishkovskaya, I.Singh, K.Schleiffer, A.Jude, J.Deswal, S.Kalis, R.Vunjak, M.Lendl, T.Imre, R.Roitinger, E.Neumann, T.Kandolf, S.Schutzbier, M.Mechtler, K.Versteeg, G.A.Haselbach, D.Zuber, J.

(2021) Nature 599: 491-496

  • DOI: https://doi.org/10.1038/s41586-021-04035-8
  • Primary Citation of Related Structures:  
    7NHT

  • PubMed 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 ...

    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 1-3 . 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.


    Organizational Affiliation

    Medical University of Vienna, Vienna BioCenter (VBC), Vienna, Austria. johannes.zuber@imp.ac.at.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2A234Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
UniProt & NIH Common Fund Data Resources
Find proteins for P25787 (Homo sapiens)
Explore P25787 
Go to UniProtKB:  P25787
PHAROS:  P25787
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25787
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4B261Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
UniProt & NIH Common Fund Data Resources
Find proteins for P25789 (Homo sapiens)
Explore P25789 
Go to UniProtKB:  P25789
PHAROS:  P25789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25789
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7C248Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
UniProt & NIH Common Fund Data Resources
Find proteins for O14818 (Homo sapiens)
Explore O14818 
Go to UniProtKB:  O14818
PHAROS:  O14818
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14818
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
UniProt & NIH Common Fund Data Resources
Find proteins for P28066 (Homo sapiens)
Explore P28066 
Go to UniProtKB:  P28066
PHAROS:  P28066
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28066
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1E263Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens)
Explore P25786 
Go to UniProtKB:  P25786
PHAROS:  P25786
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25786
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3F255Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
UniProt & NIH Common Fund Data Resources
Find proteins for P25788 (Homo sapiens)
Explore P25788 
Go to UniProtKB:  P25788
PHAROS:  P25788
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25788
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6G246Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
UniProt & NIH Common Fund Data Resources
Find proteins for P60900 (Homo sapiens)
Explore P60900 
Go to UniProtKB:  P60900
PHAROS:  P60900
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60900
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7H277Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99436 (Homo sapiens)
Explore Q99436 
Go to UniProtKB:  Q99436
PHAROS:  Q99436
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99436
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49720 (Homo sapiens)
Explore P49720 
Go to UniProtKB:  P49720
PHAROS:  P49720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49720
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2J201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49721 (Homo sapiens)
Explore P49721 
Go to UniProtKB:  P49721
PHAROS:  P49721
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49721
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5K263Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28074 (Homo sapiens)
Explore P28074 
Go to UniProtKB:  P28074
PHAROS:  P28074
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28074
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1L241Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P20618 (Homo sapiens)
Explore P20618 
Go to UniProtKB:  P20618
PHAROS:  P20618
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20618
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4M264Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28070 (Homo sapiens)
Explore P28070 
Go to UniProtKB:  P28070
PHAROS:  P28070
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28070
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6N239Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28072 (Homo sapiens)
Explore P28072 
Go to UniProtKB:  P28072
PHAROS:  P28072
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28072
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Akirin-2O [auth c],
P [auth d]
203Homo sapiensMutation(s): 0 
Gene Names: AKIRIN2C6orf166
UniProt & NIH Common Fund Data Resources
Find proteins for Q53H80 (Homo sapiens)
Explore Q53H80 
Go to UniProtKB:  Q53H80
PHAROS:  Q53H80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53H80
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download Ideal Coordinates CCD File 
Q [auth G],
R [auth L],
S [auth N]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTREFMAC
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-01
    Type: Initial release
  • Version 1.1: 2021-11-17
    Changes: Data collection, Database references
  • Version 1.2: 2021-12-01
    Changes: Database references