6HVT

Yeast 20S proteasome with human beta2i (1-53) in complex with 20

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


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Literature

Structure-Based Design of Inhibitors Selective for Human Proteasome beta 2c or beta 2i Subunits.

Xin, B.T., Huber, E.M., de Bruin, G., Heinemeyer, W., Maurits, E., Espinal, C., Du, Y., Janssens, M., Weyburne, E.S., Kisselev, A.F., Florea, B.I., Driessen, C., van der Marel, G.A., Groll, M., Overkleeft, H.S.

(2019) J Med Chem 62: 1626-1642

  • DOI: 10.1021/acs.jmedchem.8b01884
  • Primary Citation of Related Structures:  
    6HUB, 6HTR, 6HTP, 6HTC, 6HTB, 6HTD, 6HVA, 6HV5, 6HV4, 6HUV

  • PubMed Abstract: 

    • Subunit-selective proteasome inhibitors are valuable tools to assess the biological and medicinal relevance of individual proteasome active sites. Whereas the inhibitors for the β1c, β1i, β5c, and β5i subunits exploit the differences in the substrate-bin ...

    Subunit-selective proteasome inhibitors are valuable tools to assess the biological and medicinal relevance of individual proteasome active sites. Whereas the inhibitors for the β1c, β1i, β5c, and β5i subunits exploit the differences in the substrate-binding channels identified by X-ray crystallography, compounds selectively targeting β2c or β2i could not yet be rationally designed because of the high structural similarity of these two subunits. Here, we report the development, chemical synthesis, and biological screening of a compound library that led to the identification of the β2c- and β2i-selective compounds LU-002c (4; IC 50 β2c: 8 nM, IC 50 β2i/β2c: 40-fold) and LU-002i (5; IC 50 β2i: 220 nM, IC 50 β2c/β2i: 45-fold), respectively. Co-crystal structures with β2 humanized yeast proteasomes visualize protein-ligand interactions crucial for subunit specificity. Altogether, organic syntheses, activity-based protein profiling, yeast mutagenesis, and structural biology allowed us to decipher significant differences of β2 substrate-binding channels and to complete the set of subunit-selective proteasome inhibitors.

    Organizational Affiliation: 

    Gorlaeus Laboratories , Leiden Institute of Chemistry and Netherlands Proteomics Centre , Einsteinweg 55 , 2333 CC Leiden , Netherlands.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2 A, O250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE8, PRS4, YML092C
EC: 3.4.25.1
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3 B, P258Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE9, PRS5, YGR135W
EC: 3.4.25.1
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4 C, Q254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE6, YOL038W
EC: 3.4.25.1
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5 D, R260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP2, DOA5, YGR253C, G9155
EC: 3.4.25.1
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6 E, S234Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE5, YMR314W, YM9924.06
EC: 3.4.25.1
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Probable proteasome subunit alpha type-7 F, T288Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE10, PRC1, PRS1, YOR362C, O6650
EC: 3.4.25.1
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1 G, U252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SCL1, PRC2, PRS2, YGL011C
EC: 3.4.25.1
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-10,Proteasome subunit beta type-2 H, V226Homo sapiens, Saccharomyces cerevisiae S288C
This entity is chimeric		Mutation(s): 0 
Gene Names: PSMB10, LMP10, MECL1
EC: 3.4.25.1
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Find proteins for P40306 (Homo sapiens)
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NIH Common Fund Data Resources
PHAROS:  P40306
GTEx:  ENSG00000205220
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-3 I, W205Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PUP3, YER094C
EC: 3.4.25.1
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-4 J, X198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE1, YER012W
EC: 3.4.25.1
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-5 K, Y212Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE2, DOA3, PRG1, YPR103W, P8283.10
EC: 3.4.25.1
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-6 L, Z222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE7, PRS3, PTS1, YBL041W, YBL0407
EC: 3.4.25.1
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-7 M, a246Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE4, YFR050C
EC: 3.4.25.1
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome subunit beta type-1 N, b196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRE3, YJL001W, J1407
EC: 3.4.25.1
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.56α = 90
b = 300.05β = 112.92
c = 144.5γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACphasing
REFMACrefinement

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-11 
  • Released Date: 2019-01-30 
    • Deposition Author(s): Huber, E.M., Groll, M.
Funding OrganizationLocationGrant Number
German Research FoundationGermanyGR1861/10-1

Revision History 

  • Version 1.0: 2019-01-30
    Type: Initial release
  • Version 1.1: 2019-04-24
    Changes: Data collection, Database references