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



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
  • Structures With Same Primary Citation

  • 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 ...

    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: 3
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-7
C, Q
248Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
Go to UniProtKB:  O14818
NIH Common Fund Data Resources
PHAROS  O14818
GTEx  ENSG00000101182

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-1
E, S
263Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
Go to UniProtKB:  P25786
NIH Common Fund Data Resources
PHAROS  P25786
GTEx  ENSG00000129084

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-2
A, O
234Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
Go to UniProtKB:  P25787
NIH Common Fund Data Resources
PHAROS  P25787
GTEx  ENSG00000106588

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-2
J, X
201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
Go to UniProtKB:  P49721
NIH Common Fund Data Resources
PHAROS  P49721
GTEx  ENSG00000126067

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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
K, Y
263Homo sapiensMutation(s): 0 
Gene Names: PSMB5, LMPX, MB1, X
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
Go to UniProtKB:  P28074
NIH Common Fund Data Resources
PHAROS  P28074
GTEx  ENSG00000100804

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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
L, Z
241Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
Go to UniProtKB:  P20618
NIH Common Fund Data Resources
PHAROS  P20618
GTEx  ENSG00000008018

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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
M, a
264Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
Go to UniProtKB:  P28070
NIH Common Fund Data Resources
PHAROS  P28070
GTEx  ENSG00000159377

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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
N, b
239Homo sapiensMutation(s): 0 
Gene Names: PSMB6, LMPY, Y
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
Go to UniProtKB:  P28072
NIH Common Fund Data Resources
PHAROS  P28072
GTEx  ENSG00000142507

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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Proteasome activator complex subunit 4
c
1878Homo sapiensMutation(s): 0 
Gene Names: PSME4, KIAA0077
Find proteins for Q14997 (Homo sapiens)
Go to UniProtKB:  Q14997
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PHAROS  Q14997
GTEx  ENSG00000068878

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-4
B, P
261Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
Go to UniProtKB:  P25789
NIH Common Fund Data Resources
PHAROS  P25789
GTEx  ENSG00000041357

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-5
D, R
241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
Go to UniProtKB:  P28066
NIH Common Fund Data Resources
PHAROS  P28066
GTEx  ENSG00000143106

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-3
F, T
255Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
Go to UniProtKB:  P25788
NIH Common Fund Data Resources
PHAROS  P25788
GTEx  ENSG00000100567

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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit alpha type-6
G, U
246Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
Go to UniProtKB:  P60900
NIH Common Fund Data Resources
PHAROS  P60900
GTEx  ENSG00000100902

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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
H, V
277Homo sapiensMutation(s): 0 
Gene Names: PSMB7, Z
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
Go to UniProtKB:  Q99436
NIH Common Fund Data Resources
PHAROS  Q99436
GTEx  ENSG00000136930

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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-3
I, W
205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
Go to UniProtKB:  P49720
NIH Common Fund Data Resources
PHAROS  P49720
GTEx  ENSG00000277791
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K0W
Query on K0W
Download CCD File 
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
I6P
Query on I6P
Download CCD File 
c
INOSITOL 1,2,3,4,5,6-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

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

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

Revision History 

  • Version 1.0: 2020-04-01
    Type: Initial release