5LE5

Native human 20S proteasome at 1.8 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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, 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-2A, O234Homo sapiensMutation(s): 0 
Gene Names: PSMA2HC3PSC3
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4B, P261Homo sapiensMutation(s): 0 
Gene Names: PSMA4HC9PSC9
EC: 3.4.25.1
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PHAROS:  P25789
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7C, Q248Homo sapiensMutation(s): 0 
Gene Names: PSMA7HSPC
EC: 3.4.25.1
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PHAROS:  O14818
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D, R241Homo sapiensMutation(s): 0 
Gene Names: PSMA5
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1E, S263Homo sapiensMutation(s): 0 
Gene Names: PSMA1HC2NUPROS30PSC2
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3F, T255Homo sapiensMutation(s): 0 
Gene Names: PSMA3HC8PSC8
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6G, U246Homo sapiensMutation(s): 0 
Gene Names: PSMA6PROS27
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7H, V234Homo sapiensMutation(s): 0 
Gene Names: PSMB7Z
EC: 3.4.25.1
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3I, W205Homo sapiensMutation(s): 0 
Gene Names: PSMB3
EC: 3.4.25.1
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-2J, X201Homo sapiensMutation(s): 0 
Gene Names: PSMB2
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5K, Y204Homo sapiensMutation(s): 0 
Gene Names: PSMB5LMPXMB1X
EC: 3.4.25.1
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Find proteins for P28074 (Homo sapiens)
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1L, Z213Homo sapiensMutation(s): 0 
Gene Names: PSMB1PSC5
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4M, AA [auth a]219Homo sapiensMutation(s): 0 
Gene Names: PSMB4PROS26
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6N, BA [auth b]205Homo sapiensMutation(s): 0 
Gene Names: PSMB6LMPYY
EC: 3.4.25.1
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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 
AB [auth I] , BB [auth I] , DD [auth b] , ED [auth b] , JB [auth L] , NC [auth W] , SA [auth G] , UC [auth Z] , 
AB [auth I], BB [auth I], DD [auth b], ED [auth b], JB [auth L], NC [auth W], SA [auth G], UC [auth Z], ZC [auth a]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
FD [auth b], HC [auth U], KB [auth L], TA [auth G], TB [auth N], VC [auth Z]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
AC [auth Q] , AD [auth b] , BC [auth R] , BD [auth b] , CA [auth A] , CC [auth R] , CD [auth b] , DA [auth A] , 
AC [auth Q], AD [auth b], BC [auth R], BD [auth b], CA [auth A], CC [auth R], CD [auth b], DA [auth A], DC [auth S], EA [auth A], EC [auth S], FA [auth A], FB [auth K], FC [auth S], GA [auth B], GB [auth K], GC [auth U], HA [auth B], HB [auth K], IA [auth C], IB [auth K], JA [auth C], JC [auth V], KA [auth D], KC [auth V], LA [auth D], MA [auth E], MB [auth M], MC [auth W], NA [auth E], NB [auth M], OA [auth E], OB [auth M], PA [auth F], PB [auth M], PC [auth Y], QA [auth G], QB [auth N], QC [auth Y], RA [auth G], RB [auth N], RC [auth Y], SB [auth N], SC [auth Y], TC [auth Y], UB [auth O], VB [auth O], WA [auth H], WB [auth O], WC [auth a], XA [auth H], XB [auth O], XC [auth a], YB [auth P], YC [auth a], ZA [auth I], ZB [auth Q]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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CB [auth I] , DB [auth J] , EB [auth K] , IC [auth V] , LB [auth L] , LC [auth W] , OC [auth X] , UA [auth H] , 
CB [auth I], DB [auth J], EB [auth K], IC [auth V], LB [auth L], LC [auth W], OC [auth X], UA [auth H], VA [auth H], YA [auth I]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.44α = 90
b = 202.77β = 90
c = 316γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

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  (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