5LF7

Human 20S proteasome complex with Ixazomib at 2.0 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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 für biophysikalische Chemie, Am Fassberg 11, D-37077 Göttingen, 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
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PHAROS:  P25787
GTEx:  ENSG00000106588 
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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
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PHAROS:  P25789
GTEx:  ENSG00000041357 
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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
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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
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GTEx:  ENSG00000143106 
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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
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GTEx:  ENSG00000129084 
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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
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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
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GTEx:  ENSG00000100902 
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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
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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
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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
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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
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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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GTEx:  ENSG00000008018 
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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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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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GTEx:  ENSG00000142507 
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6V8
Query on 6V8

Download Ideal Coordinates CCD File 
FD [auth b]
IB [auth K]
MC [auth V]
VB [auth N]
WC [auth Y]
FD [auth b],
IB [auth K],
MC [auth V],
VB [auth N],
WC [auth Y],
XA [auth H]
[(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
1PE
Query on 1PE

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AB [auth I]
BB [auth I]
DD [auth b]
JB [auth L]
PC [auth W]
AB [auth I],
BB [auth I],
DD [auth b],
JB [auth L],
PC [auth W],
QB [auth M],
TB [auth N],
VC [auth Y],
WA [auth H]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
K
Query on K

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ED [auth b]
JC [auth U]
KB [auth L]
SA [auth G]
UB [auth N]
ED [auth b],
JC [auth U],
KB [auth L],
SA [auth G],
UB [auth N],
XC [auth Z]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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AC [auth P]
AD [auth a]
BC [auth Q]
BD [auth a]
CA [auth A]
AC [auth P],
AD [auth a],
BC [auth Q],
BD [auth a],
CA [auth A],
CC [auth Q],
CD [auth b],
DA [auth A],
DC [auth R],
EA [auth A],
EC [auth R],
FA [auth A],
FB [auth K],
FC [auth S],
GA [auth B],
GB [auth K],
GC [auth S],
HA [auth B],
HB [auth K],
HC [auth S],
IA [auth C],
IC [auth U],
JA [auth C],
KA [auth D],
LA [auth D],
LC [auth V],
MA [auth E],
MB [auth M],
NA [auth E],
NB [auth M],
OA [auth E],
OB [auth M],
OC [auth W],
PA [auth F],
PB [auth M],
QA [auth G],
RA [auth G],
RB [auth N],
RC [auth Y],
SB [auth N],
SC [auth Y],
TC [auth Y],
UC [auth Y],
VA [auth H],
WB [auth O],
XB [auth O],
YB [auth O],
YC [auth a],
ZA [auth I],
ZB [auth O],
ZC [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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CB [auth I]
DB [auth J]
EB [auth K]
KC [auth V]
LB [auth L]
CB [auth I],
DB [auth J],
EB [auth K],
KC [auth V],
LB [auth L],
NC [auth W],
QC [auth X],
TA [auth H],
UA [auth H],
YA [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 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
Binding Affinity Annotations 
IDSourceBinding Affinity
6V8 BindingDB:  5LF7 IC50: min: 3, max: 3500 (nM) from 6 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.41α = 90
b = 202.61β = 90
c = 314.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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: 2016-12-21
    Changes: Structure summary
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description