5LEY

Human 20S proteasome complex with Oprozomib at 1.9 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 ?
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/10.1126/science.aaf8993
  • Primary Citation of Related Structures:  
    5LE5, 5LEX, 5LEY, 5LEZ, 5LF0, 5LF1, 5LF3, 5LF4, 5LF6, 5LF7

  • 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 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 f¨¹r biophysikalische Chemie, Am Fassberg 11, D-37077 G?ttingen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2
A, O
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25787 (Homo sapiens)
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PHAROS:  P25787
GTEx:  ENSG00000106588 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25787
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
B, P
261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25789 (Homo sapiens)
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PHAROS:  P25789
GTEx:  ENSG00000041357 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25789
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
C, Q
248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for O14818 (Homo sapiens)
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PHAROS:  O14818
GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
D, R
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28066 (Homo sapiens)
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PHAROS:  P28066
GTEx:  ENSG00000143106 
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UniProt GroupP28066
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
E, S
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens)
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PHAROS:  P25786
GTEx:  ENSG00000129084 
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UniProt GroupP25786
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
F, T
255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P25788 (Homo sapiens)
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PHAROS:  P25788
GTEx:  ENSG00000100567 
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UniProt GroupP25788
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
G, U
246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P60900 (Homo sapiens)
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PHAROS:  P60900
GTEx:  ENSG00000100902 
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UniProt GroupP60900
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7
H, V
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99436 (Homo sapiens)
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PHAROS:  Q99436
GTEx:  ENSG00000136930 
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UniProt GroupQ99436
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
I, W
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49720 (Homo sapiens)
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PHAROS:  P49720
GTEx:  ENSG00000277791 
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UniProt GroupP49720
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
J, X
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
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GTEx:  ENSG00000126067 
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UniProt GroupP49721
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5
K, Y
204Homo sapiensMutation(s): 0 
EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28074 (Homo sapiens)
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GTEx:  ENSG00000100804 
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UniProt GroupP28074
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1
L, Z
213Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P20618 (Homo sapiens)
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GTEx:  ENSG00000008018 
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UniProt GroupP20618
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4AA [auth a],
M
219Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P28070 (Homo sapiens)
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GTEx:  ENSG00000159377 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6BA [auth b],
N
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P28072 (Homo sapiens)
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GTEx:  ENSG00000142507 
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UniProt GroupP28072
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
bound OprozomibCA [auth c],
DA [auth d]
4synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
AB [auth H]
DB [auth I]
EB [auth I]
MB [auth L]
PC [auth V]
AB [auth H],
DB [auth I],
EB [auth I],
MB [auth L],
PC [auth V],
SC [auth W],
TB [auth M],
ZA [auth H],
ZC [auth Z]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
K
Query on K

Download Ideal Coordinates CCD File 
AD [auth Z]
ID [auth b]
LC [auth U]
NB [auth L]
UA [auth G]
AD [auth Z],
ID [auth b],
LC [auth U],
NB [auth L],
UA [auth G],
XB [auth N]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AC [auth O]
BC [auth O]
BD [auth a]
CB [auth I]
CC [auth P]
AC [auth O],
BC [auth O],
BD [auth a],
CB [auth I],
CC [auth P],
CD [auth a],
DC [auth Q],
DD [auth a],
EA [auth A],
EC [auth Q],
ED [auth b],
FA [auth A],
FC [auth R],
FD [auth b],
GA [auth A],
GC [auth R],
GD [auth b],
HA [auth A],
HC [auth S],
HD [auth b],
IA [auth B],
IB [auth K],
IC [auth S],
JA [auth B],
JB [auth K],
JC [auth S],
KA [auth C],
KB [auth K],
KC [auth U],
LA [auth C],
LB [auth K],
MA [auth D],
NA [auth D],
NC [auth V],
OA [auth E],
OC [auth V],
PA [auth E],
PB [auth M],
QA [auth E],
QB [auth M],
RA [auth F],
RB [auth M],
RC [auth W],
SA [auth G],
SB [auth M],
TA [auth G],
UB [auth N],
UC [auth Y],
VB [auth N],
VC [auth Y],
WB [auth N],
WC [auth Y],
XA [auth H],
XC [auth Y],
YA [auth H],
YB [auth O],
YC [auth Y],
ZB [auth O]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

Download Ideal Coordinates CCD File 
BB [auth I]
FB [auth I]
GB [auth J]
HB [auth K]
MC [auth V]
BB [auth I],
FB [auth I],
GB [auth J],
HB [auth K],
MC [auth V],
OB [auth L],
QC [auth W],
TC [auth X],
VA [auth H],
WA [auth H]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
YCM
Query on YCM
C, Q
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
6V1
Query on 6V1
E, S
L-PEPTIDE LINKINGC9 H14 N2 O4 SCYS
OAS
Query on OAS
CA [auth c],
DA [auth d]
L-PEPTIDE LINKINGC5 H9 N O4SER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 ?
  • R-Value Free: 0.225 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length ( ? )Angle ( ? )
a = 113.39¦Á = 90
b = 202.65¦Â = 90
c = 315.14¦Ã = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



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  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2024-01-10
    Changes: Refinement description
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