5LF7

Human 20S proteasome complex with Ixazomib at 2.0 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The inhibition mechanism of human 20S proteasomes enables next-generation inhibitor design.

Schrader, J.Henneberg, F.Mata, R.A.Tittmann, K.Schneider, T.R.Stark, H.Bourenkov, G.Chari, A.

(2016) Science 353: 594-598

  • DOI: 10.1126/science.aaf8993
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The proteasome is a validated target for anticancer therapy, and proteasome inhibition is employed in the clinic for the treatment of tumors and hematological malignancies. Here, we describe crystal structures of the native human 20S proteasome and i ...

    The proteasome is a validated target for anticancer therapy, and proteasome inhibition is employed in the clinic for the treatment of tumors and hematological malignancies. Here, we describe crystal structures of the native human 20S proteasome and its complexes with inhibitors, which either are drugs approved for cancer treatment or are in clinical trials. The structure of the native human 20S proteasome was determined at an unprecedented resolution of 1.8 angstroms. Additionally, six inhibitor-proteasome complex structures were elucidated at resolutions between 1.9 and 2.1 angstroms. Collectively, the high-resolution structures provide new insights into the catalytic mechanisms of inhibition and necessitate a revised description of the proteasome active site. Knowledge about inhibition mechanisms provides insights into peptide hydrolysis and can guide strategies for the development of next-generation proteasome-based cancer therapeutics.


    Organizational Affiliation

    Department of Structural Dynamics, Max Planck Institut für biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

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 Gene View: PSMA2
Go to UniProtKB:  P25787
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 Gene View: PSMA4
Go to UniProtKB:  P25789
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 Gene View: PSMA7
Go to UniProtKB:  O14818
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 Gene View: PSMA5
Go to UniProtKB:  P28066
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 Gene View: PSMA1
Go to UniProtKB:  P25786
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 Gene View: PSMA3
Go to UniProtKB:  P25788
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 Gene View: PSMA6
Go to UniProtKB:  P60900
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-7
H, V
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: 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 Gene View: PSMB3
Go to UniProtKB:  P49720
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 Gene View: PSMB2
Go to UniProtKB:  P49721
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-5
K, Y
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: 12
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-1
L, Z
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: 13
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-4
M, a
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
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Proteasome subunit beta type-6
N, b
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
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
b, G, L, N, U, Z
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, a, B, b, C, D, E, F, G, H, I, K, M, N, O, P, Q, R, S, U, V, W, Y
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
6V8
Query on 6V8

Download SDF File 
Download CCD File 
b, H, K, N, V, Y
[(1~{R})-1-[2-[[2,5-bis(chloranyl)phenyl]carbonylamino]ethanoylamino]-3-methyl-butyl]boronic acid
C14 H19 B Cl2 N2 O4
MXAYKZJJDUDWDS-LBPRGKRZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
H, I, J, K, L, V, W, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
1PE
Query on 1PE

Download SDF File 
Download CCD File 
b, H, I, L, M, N, W, Y
PENTAETHYLENE GLYCOL
PEG400
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
C, G, Q, U
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
6V1
Query on 6V1
E, G, J, S, U, X
L-PEPTIDE LINKINGC9 H14 N2 O4 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6V8IC50: 3.4 - 3500 nM (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 113.410α = 90.00
b = 202.610β = 90.00
c = 314.510γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyCH1098/1-1
German Research FoundationGermanySFB860-TP A5
Bundesministerium fuer Bildung und ForschungGermany05K2013-624

Revision History 

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-12-21
    Type: Structure summary
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence, Data collection