5A0Q

Cryo-EM reveals the conformation of a substrate analogue in the human 20S proteasome core

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Cryo-Em Reveals the Conformation of a Substrate Analogue in the Human 20S Proteasome Core.

Da Fonseca, P.C.A., Morris, E.P.

(2015) Nat Commun 6: 7573

  • DOI: 10.1038/ncomms8573
  • Primary Citation of Related Structures:  
    5A0Q

  • PubMed Abstract: 

    • The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3 ...

    The proteasome is a highly regulated protease complex fundamental for cell homeostasis and controlled cell cycle progression. It functions by removing a wide range of specifically tagged proteins, including key cellular regulators. Here we present the structure of the human 20S proteasome core bound to a substrate analogue inhibitor molecule, determined by electron cryo-microscopy (cryo-EM) and single-particle analysis at a resolution of around 3.5 Å. Our map allows the building of protein coordinates as well as defining the location and conformation of the inhibitor at the different active sites. These results open new prospects to tackle the proteasome functional mechanisms. Moreover, they also further demonstrate that cryo-EM is emerging as a realistic approach for general structural studies of protein-ligand interactions.

    Organizational Affiliation: 

    Division of Structural Biology, The Institute of Cancer Research, London SW3 3RP, UK.



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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEASOME SUBUNIT ALPHA TYPE-6A, O246Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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PROTEASOME SUBUNIT ALPHA TYPE-2B, P234Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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PROTEASOME SUBUNIT ALPHA TYPE-4C, Q261Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
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Entity ID: 4
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PROTEASOME SUBUNIT ALPHA TYPE-7D, R248Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
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Entity ID: 5
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PROTEASOME SUBUNIT ALPHA TYPE-5E, S241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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PROTEASOME SUBUNIT ALPHA TYPE-1F, T263Homo sapiensMutation(s): 0 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
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PROTEASOME SUBUNIT ALPHA TYPE-3G, U255Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
EC: 3.4.25.1
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PROTEASOME SUBUNIT BETA TYPE-6H, V205Homo sapiensMutation(s): 0 
Gene Names: PSMB6, LMPY, Y
EC: 3.4.25.1
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PROTEASOME SUBUNIT BETA TYPE-7I, W234Homo sapiensMutation(s): 0 
Gene Names: PSMB7, Z
EC: 3.4.25.1
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PROTEASOME SUBUNIT BETA TYPE-3J, X204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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PROTEASOME SUBUNIT BETA TYPE-2K, Y201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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PROTEASOME SUBUNIT BETA TYPE-5L, Z204Homo sapiensMutation(s): 0 
Gene Names: PSMB5, LMPX, MB1, X
EC: 3.4.25.1
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PROTEASOME SUBUNIT BETA TYPE-1M,
AA [auth a]		213Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
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PROTEASOME SUBUNIT BETA TYPE-4N,
BA [auth b]		219Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KNM
Query on KNM
Download Ideal Coordinates CCD File 
CA [auth H],
DA [auth I],
EA [auth L],
FA [auth V],
GA [auth W],
CA [auth H],
DA [auth I],
EA [auth L],
FA [auth V],
GA [auth W],
HA [auth Z]
ADA-(AHX)3-(LEU)3-VINYL SULFONE
C51 H92 N6 O8 S
BVBBFBDIMMETKA-GNKIUVBNSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2017-08-02
    Changes: Data collection