4QXJ

yCP beta5-M45A mutant in complex with the epoxyketone inhibitor ONX 0914

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


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Literature

Bortezomib-Resistant Mutant Proteasomes: Structural and Biochemical Evaluation with Carfilzomib and ONX 0914.

Huber, E.M., Heinemeyer, W., Groll, M.

(2015) Structure 23: 407-417

  • DOI: https://doi.org/10.1016/j.str.2014.11.019
  • Primary Citation of Related Structures:  
    4QUX, 4QUY, 4QV0, 4QV1, 4QV3, 4QV4, 4QV5, 4QV6, 4QV7, 4QV8, 4QV9, 4QVL, 4QVM, 4QVN, 4QVP, 4QVQ, 4QVV, 4QVW, 4QVY, 4QW0, 4QW1, 4QW3, 4QW4, 4QW5, 4QW6, 4QW7, 4QWF, 4QWG, 4QWI, 4QWJ, 4QWK, 4QWL, 4QWR, 4QWS, 4QWU, 4QWX, 4QXJ, 4QZ0, 4QZ1, 4QZ2, 4QZ3, 4QZ4, 4QZ5, 4QZ6, 4QZ7, 4QZW, 4QZX, 4QZZ, 4R00

  • PubMed Abstract: 

    • Inhibition of the 20S proteasome by bortezomib (Velcade) constitutes a successfully applied therapy for blood cancer. However, emerging resistance restricts its medicinal use. For example, mutations in the proteolytically active β5-subunit of the proteasome, the main target of inhibitors, were reported to impair drug binding and thus to reduce therapeutic efficacy ...

    Inhibition of the 20S proteasome by bortezomib (Velcade) constitutes a successfully applied therapy for blood cancer. However, emerging resistance restricts its medicinal use. For example, mutations in the proteolytically active β5-subunit of the proteasome, the main target of inhibitors, were reported to impair drug binding and thus to reduce therapeutic efficacy. Using yeast as a model system, we describe here a systematic evaluation of these mutations by cell growth analysis, proteasome inhibition assays, and X-ray crystallography. The 11 mutants examined display decreased proliferation rates, impaired proteolytic activity, and marked resistance to bortezomib as well as the α',β'-epoxyketone inhibitors carfilzomib (Kyprolis) and ONX 0914, while the second-generation compound carfilzomib was the least affected. In total, 49 proteasome X-ray structures, including structural data on proteasome-carfilzomib complexes, reveal three distinct molecular mechanisms that hamper both drug binding and natural substrate turnover to an extent that is still compatible with cell survival.

    Organizational Affiliation: 

    Center for Integrated Protein Science at the Department Chemie, Lehrstuhl für Biochemie, Technische Universität München, Lichtenbergstraße 4, 85747 Garching, Germany. Electronic address: michael.groll@tum.de.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2A, O250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8, PRS4, YML092C
EC: 3.4.25.1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3B, P258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9, PRS5, YGR135W
EC: 3.4.25.1
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4C, Q254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6, YOL038W
EC: 3.4.25.1
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5D, R260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2, DOA5, YGR253C, G9155
EC: 3.4.25.1
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6E, S234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5, YMR314W, YM9924.06
EC: 3.4.25.1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7F, T288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10, PRC1, PRS1, YOR362C, O6650
EC: 3.4.25.1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1G, U252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1, PRC2, PRS2, YGL011C
EC: 3.4.25.1
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Entity ID: 8
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Proteasome subunit beta type-2H, V232Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP1, YOR157C
EC: 3.4.25.1
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Entity ID: 9
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Proteasome subunit beta type-3I, W205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3, YER094C
EC: 3.4.25.1
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Entity ID: 10
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Proteasome subunit beta type-4J, X198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1, YER012W
EC: 3.4.25.1
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5K, Y212Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: PRE2, DOA3, PRG1, YPR103W, P8283.10
EC: 3.4.25.1
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Entity ID: 12
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Proteasome subunit beta type-6L, Z222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE7, PRS3, PTS1, YBL041W, YBL0407
EC: 3.4.25.1
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7AA [auth a],
M		246Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4, YFR050C
EC: 3.4.25.1
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MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1BA [auth b],
N		196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3, YJL001W, J1407
EC: 3.4.25.1
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Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
04C
Query on 04C
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EA [auth H],
HA [auth K],
KA [auth N],
NA [auth V],
QA [auth Y],
EA [auth H],
HA [auth K],
KA [auth N],
NA [auth V],
QA [auth Y],
TA [auth b]
1,2,4-trideoxy-4-methyl-2-{[N-(morpholin-4-ylacetyl)-L-alanyl-O-methyl-L-tyrosyl]amino}-1-phenyl-D-xylitol
C31 H44 N4 O7
SLVOSRJOLWNALP-QAKIEGLASA-N		 Ligand Interaction
MES
Query on MES
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FA [auth H],
JA [auth K],
PA [auth V],
SA [auth Y]		2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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DA [auth G],
MA [auth U]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
MG
Query on MG
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CA [auth G],
GA [auth I],
IA [auth K],
LA [auth N],
OA [auth V],
CA [auth G],
GA [auth I],
IA [auth K],
LA [auth N],
OA [auth V],
RA [auth Y]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 17
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000991 (04C)
Query on PRD_000991
EA [auth H] , HA [auth K] , KA [auth N] , NA [auth V] , QA [auth Y] , 
EA [auth H], HA [auth K], KA [auth N], NA [auth V], QA [auth Y], TA [auth b]
1,2,4-TRIDEOXY-4-METHYL-2-{[N-(MORPHOLIN-4-YLACETYL)-L-ALANYL-O-METHYL-L-TYROSYL]AMINO}-1-PHENYL-D-XYLITOLPeptide-like / Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.49α = 90
b = 299.73β = 113.16
c = 145.61γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-04
    Type: Initial release
  • Version 1.1: 2015-02-18
    Changes: Database references