5LF0

Human 20S proteasome complex with Epoxomicin at 2.4 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    5LE5, 5LF7, 5LEY, 5LEX, 5LEZ, 5LF0, 5LF1, 5LF4, 5LF3, 5LF6

  • 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 its c ...

    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. ashwin.chari@mpibpc.mpg.de gleb@embl-hamburg.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2 AO234Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
Find proteins for P25787 (Homo sapiens)
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4 BP261Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
Find proteins for P25789 (Homo sapiens)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7 CQ248Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
Find proteins for O14818 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5 DR241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
Find proteins for P28066 (Homo sapiens)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1 ES263Homo sapiensMutation(s): 1 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
Find proteins for P25786 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3 FT255Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
Find proteins for P25788 (Homo sapiens)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6 GU246Homo sapiensMutation(s): 2 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
Find proteins for P60900 (Homo sapiens)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7 HV234Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
Find proteins for Q99436 (Homo sapiens)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3 IW205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
Find proteins for P49720 (Homo sapiens)
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PHAROS:  P49720
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2 JX201Homo sapiensMutation(s): 1 
Gene Names: PSMB2
EC: 3.4.25.1
Find proteins for P49721 (Homo sapiens)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5 KY204Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
Find proteins for P28074 (Homo sapiens)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1 LZ213Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
Find proteins for P20618 (Homo sapiens)
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4 Ma219Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
Find proteins for P28070 (Homo sapiens)
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6 Nb205Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
Find proteins for P28072 (Homo sapiens)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
EPOXOMICIN (peptide inhibitor) cdefgh5synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
H, I, K, L, N, W, Z, a, b
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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

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

Download Ideal Coordinates CCD File 
H, I, J, K, L, V, W, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
C,QL-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
6V1
Query on 6V1
E,SL-PEPTIDE LINKINGC9 H14 N2 O4 SCYS
IML
Query on IML
c,d,e,f,g,hL-PEPTIDE LINKINGC7 H15 N O2ILE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.07α = 90
b = 202.37β = 90
c = 314.79γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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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: 2017-09-06
    Changes: Author supporting evidence, Data collection