6KWY

human PA200-20S complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Cryo-EM structures of the human PA200 and PA200-20S complex reveal regulation of proteasome gate opening and two PA200 apertures.

Guan, H.Wang, Y.Yu, T.Huang, Y.Li, M.Saeed, A.F.U.H.Perculija, V.Li, D.Xiao, J.Wang, D.Zhu, P.Ouyang, S.

(2020) PLoS Biol 18: e3000654-e3000654

  • DOI: 10.1371/journal.pbio.3000654
  • Primary Citation of Related Structures:  
    6KWX, 6KWY

  • PubMed Abstract: 
  • Proteasomes are highly abundant and conserved protease complexes that eliminate unwanted proteins in the cells. As a single-chain ATP-independent nuclear proteasome activator, proteasome activator 200 (PA200) associates with 20S core particle to form proteasome complex that catalyzes polyubiquitin-independent degradation of acetylated histones, thus playing a pivotal role in DNA repair and spermatogenesis ...

    Proteasomes are highly abundant and conserved protease complexes that eliminate unwanted proteins in the cells. As a single-chain ATP-independent nuclear proteasome activator, proteasome activator 200 (PA200) associates with 20S core particle to form proteasome complex that catalyzes polyubiquitin-independent degradation of acetylated histones, thus playing a pivotal role in DNA repair and spermatogenesis. Here, we present cryo-electron microscopy (cryo-EM) structures of the human PA200-20S complex and PA200 at 2.72 Å and 3.75 Å, respectively. PA200 exhibits a dome-like architecture that caps 20S and uses its C-terminal YYA (Tyr-Tyr-Ala) to induce the α-ring rearrangements and partial opening of the 20S gate. Our structural data also indicate that PA200 has two openings formed by numerous positively charged residues that respectively bind (5,6)-bisdiphosphoinositol tetrakisphosphate (5,6[PP]2-InsP4) and inositol hexakisphosphate (InsP6) and are likely to be the gates that lead unfolded proteins through PA200 and into the 20S. Besides, our structural analysis of PA200 found that the bromodomain (BRD)-like (BRDL) domain of PA200 shows considerable sequence variation in comparison to other human BRDs, as it contains only 82 residues because of a short ZA loop, and cannot be classified into any of the eight typical human BRD families. Taken together, the results obtained from this study provide important insights into human PA200-induced 20S gate opening for substrate degradation and the opportunities to explore the mechanism for its recognition of H4 histone in acetylation-mediated proteasomal degradation.


    Organizational Affiliation

    Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2A, O234Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Find proteins for P25787 (Homo sapiens)
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PHAROS:  P25787
GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4B, P261Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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Find proteins for P25789 (Homo sapiens)
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GTEx:  ENSG00000041357 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7C, Q248Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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PHAROS:  O14818
GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D, R241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1E, S263Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3F, T255Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6G, U246Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7H, V277Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I, W205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Find proteins for P49720 (Homo sapiens)
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GTEx:  ENSG00000277791 
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2J, X201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5K, Y263Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Find proteins for P28074 (Homo sapiens)
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GTEx:  ENSG00000100804 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1L, Z241Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4M,
AA [auth a]
264Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6N,
BA [auth b]
239Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome activator complex subunit 4CA [auth c]1878Homo sapiensMutation(s): 0 
Gene Names: PSME4KIAA0077
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GTEx:  ENSG00000068878 
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Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K0W (Subject of Investigation/LOI)
Query on K0W

Download Ideal Coordinates CCD File 
DA [auth c][(1~{S},2~{R},3~{R},4~{S},5~{S},6~{R})-2-[oxidanyl(phosphonooxy)phosphoryl]oxy-3,4,5,6-tetraphosphonooxy-cyclohexyl] phosphono hydrogen phosphate
C6 H20 O30 P8
GXPFHIDIIMSLOF-FTYOSCRSSA-N
 Ligand Interaction
IHP (Subject of Investigation/LOI)
Query on IHP

Download Ideal Coordinates CCD File 
EA [auth c]INOSITOL HEXAKISPHOSPHATE
C6 H18 O24 P6
IMQLKJBTEOYOSI-GPIVLXJGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31770948

Revision History  (Full details and data files)

  • Version 1.0: 2020-04-01
    Type: Initial release
  • Version 2.0: 2020-10-14
    Changes: Advisory, Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary