5A0Q

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

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.5 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

  • 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 th ...

    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: 

    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE-6
A, O
246Homo sapiensMutation(s): 0 
Gene Names: PSMA6 (PROS27)
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
Go to Gene View: PSMA6
Go to UniProtKB:  P60900
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE-2
B, P
234Homo sapiensMutation(s): 0 
Gene Names: PSMA2 (HC3, PSC3)
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
Go to Gene View: PSMA2
Go to UniProtKB:  P25787
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE-4
C, Q
261Homo sapiensMutation(s): 0 
Gene Names: PSMA4 (HC9, PSC9)
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
Go to Gene View: PSMA4
Go to UniProtKB:  P25789
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE-7
D, R
248Homo sapiensMutation(s): 0 
Gene Names: PSMA7 (HSPC)
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
Go to Gene View: PSMA7
Go to UniProtKB:  O14818
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE-5
E, S
241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
Go to Gene View: PSMA5
Go to UniProtKB:  P28066
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE-1
F, T
263Homo sapiensMutation(s): 0 
Gene Names: PSMA1 (HC2, NU, PROS30, PSC2)
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
Go to Gene View: PSMA1
Go to UniProtKB:  P25786
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT ALPHA TYPE-3
G, U
255Homo sapiensMutation(s): 0 
Gene Names: PSMA3 (HC8, PSC8)
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
Go to Gene View: PSMA3
Go to UniProtKB:  P25788
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE-6
H, V
205Homo sapiensMutation(s): 0 
Gene Names: PSMB6 (LMPY, Y)
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
Go to Gene View: PSMB6
Go to UniProtKB:  P28072
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE-7
I, W
234Homo sapiensMutation(s): 0 
Gene Names: PSMB7 (Z)
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
Go to Gene View: PSMB7
Go to UniProtKB:  Q99436
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE-3
J, X
204Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
Go to Gene View: PSMB3
Go to UniProtKB:  P49720
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE-2
K, Y
201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
Go to Gene View: PSMB2
Go to UniProtKB:  P49721
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE-5
L, Z
204Homo sapiensMutation(s): 0 
Gene Names: PSMB5 (LMPX, MB1, X)
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
Go to Gene View: PSMB5
Go to UniProtKB:  P28074
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE-1
M, a
213Homo sapiensMutation(s): 0 
Gene Names: PSMB1 (PSC5)
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
Go to Gene View: PSMB1
Go to UniProtKB:  P20618
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
PROTEASOME SUBUNIT BETA TYPE-4
N, b
219Homo sapiensMutation(s): 0 
Gene Names: PSMB4 (PROS26)
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
Go to Gene View: PSMB4
Go to UniProtKB:  P28070
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KNM
Query on KNM
Download SDF File 
Download CCD File 
H, I, L, V, W, 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: 3.5 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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