5LF3

Human 20S proteasome complex with Bortezomib at 2.1 Angstrom

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: 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 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
A, O
234Homo sapiensMutation(s): 0 
Gene Names: PSMA2, HC3, PSC3
EC: 3.4.25.1
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PHAROS:  P25787
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UniProt GroupP25787
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4
B, P
261Homo sapiensMutation(s): 0 
Gene Names: PSMA4, HC9, PSC9
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7
C, Q
248Homo sapiensMutation(s): 0 
Gene Names: PSMA7, HSPC
EC: 3.4.25.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5
D, R
241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1
E, S
263Homo sapiensMutation(s): 1 
Gene Names: PSMA1, HC2, NU, PROS30, PSC2
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3
F, T
255Homo sapiensMutation(s): 0 
Gene Names: PSMA3, HC8, PSC8
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6
G, U
246Homo sapiensMutation(s): 0 
Gene Names: PSMA6, PROS27
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7
H, V
234Homo sapiensMutation(s): 0 
Gene Names: PSMB7, Z
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3
I, W
205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2
J, X
201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5
K, Y
204Homo sapiensMutation(s): 0 
Gene Names: PSMB5, LMPX, MB1, X
EC: 3.4.25.1
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1
L, Z
213Homo sapiensMutation(s): 0 
Gene Names: PSMB1, PSC5
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4AA [auth a],
M		219Homo sapiensMutation(s): 0 
Gene Names: PSMB4, PROS26
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6BA [auth b],
N		205Homo sapiensMutation(s): 0 
Gene Names: PSMB6, LMPY, Y
EC: 3.4.25.1
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Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BO2
Query on BO2
Download Ideal Coordinates CCD File 
FD [auth b]
JB [auth K]
MC [auth V]
VB [auth N]
VC [auth Y]
FD [auth b],
JB [auth K],
MC [auth V],
VB [auth N],
VC [auth Y],
YA [auth H]
N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
C19 H25 B N4 O4
GXJABQQUPOEUTA-RDJZCZTQSA-N		 Ligand Interaction
1PE
Query on 1PE
Download Ideal Coordinates CCD File 
BB [auth I]
CB [auth I]
DD [auth b]
KB [auth L]
PC [auth W]
BB [auth I],
CB [auth I],
DD [auth b],
KB [auth L],
PC [auth W],
RB [auth M],
WA [auth H],
WC [auth Z],
XA [auth H]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
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ED [auth b]
JC [auth U]
LB [auth L]
SA [auth G]
UB [auth N]
ED [auth b],
JC [auth U],
LB [auth L],
SA [auth G],
UB [auth N],
XC [auth Z]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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AB [auth I]
AC [auth P]
AD [auth a]
BC [auth Q]
BD [auth b]
AB [auth I],
AC [auth P],
AD [auth a],
BC [auth Q],
BD [auth b],
CA [auth A],
CC [auth Q],
CD [auth b],
DA [auth A],
DC [auth R],
EA [auth A],
EC [auth R],
FA [auth A],
FC [auth S],
GA [auth B],
GB [auth K],
GC [auth S],
HA [auth B],
HB [auth K],
HC [auth S],
IA [auth C],
IB [auth K],
IC [auth U],
JA [auth C],
KA [auth D],
LA [auth D],
LC [auth V],
MA [auth E],
NA [auth E],
NB [auth M],
OA [auth E],
OB [auth M],
OC [auth W],
PA [auth F],
PB [auth M],
QA [auth G],
QB [auth M],
RA [auth G],
RC [auth Y],
SB [auth N],
SC [auth Y],
TB [auth N],
TC [auth Y],
UC [auth Y],
VA [auth H],
WB [auth O],
XB [auth O],
YB [auth O],
YC [auth a],
ZB [auth O],
ZC [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
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DB [auth I]
EB [auth J]
FB [auth K]
KC [auth V]
MB [auth L]
DB [auth I],
EB [auth J],
FB [auth K],
KC [auth V],
MB [auth L],
NC [auth W],
QC [auth X],
TA [auth H],
UA [auth H],
ZA [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D 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
BO2 BindingDB:  5LF3 Ki: min: 0.6, max: 9.8 (nM) from 2 assay(s)
IC50: min: 0.5, max: 3998 (nM) from 38 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.37α = 90
b = 202.72β = 90
c = 314.9γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


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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  (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 1.2: 2018-11-21
    Changes: Data collection