5M2B | pdb_00005m2b

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with thiazole based inhibitor Ro19

PDB DOI: https://doi.org/10.2210/pdb5M2B/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Saccharomyces cerevisiae S288C, Homo sapiens
Expression System: Saccharomyces cerevisiae S288C
Mutation(s): No

Deposited: 2016-10-12 Released: 2017-01-25
Deposition Author(s): Groll, M.
Funding Organization(s): German Research Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.218 (Depositor), 0.221 (DCC)
R-Value Work:
0.200 (Depositor), 0.204 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structural Elucidation of a Nonpeptidic Inhibitor Specific for the Human Immunoproteasome.

Cui, H., Baur, R., Le Chapelain, C., Dubiella, C., Heinemeyer, W., Huber, E.M., Groll, M.

(2017) Chembiochem 18: 523-526

PubMed: 28098422 Search on PubMed
DOI: https://doi.org/10.1002/cbic.201700021
Primary Citation Related Structures:
5M2B

PubMed Abstract:
Selective inhibition of the immunoproteasome is a promising approach towards the development of immunomodulatory drugs. Recently, a class of substituted thiazole compounds that combine a nonpeptidic scaffold with the absence of an electrophile was reported in a patent. Here, we investigated the mode of action of the lead compound by using a sophisticated chimeric yeast model of the human immunoproteasome for structural studies. The inhibitor adopts a unique orientation perpendicular to the β5i substrate-binding channel. Distinct interactions between the inhibitor and the subpockets of the human immunoproteasome account for its isotype selectivity.

Organizational Affiliation

Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstrasse 4, 85748, Garching, Germany.

Macromolecule Content

Total Structure Weight: 732.6 kDa
Atom Count: 49,899
Modeled Residue Count: 6,342
Deposited Residue Count: 6,612
Unique protein chains: 14

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	A, O	250	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23639 Go to UniProtKB: P23639
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23639
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	B, P	258	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23638 Go to UniProtKB: P23638
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P23638
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	C, Q	254	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40303 Go to UniProtKB: P40303
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40303
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	D, R	260	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32379 Go to UniProtKB: P32379
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P32379
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	E, S	234	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40302 Go to UniProtKB: P40302
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40302
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Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable proteasome subunit alpha type-7	F, T	288	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21242 Go to UniProtKB: P21242
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21242
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	G, U	252	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21243 Go to UniProtKB: P21243
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P21243
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	H, V	232	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P25043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25043 Go to UniProtKB: P25043
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25043
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Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	I, W	205	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25451 Go to UniProtKB: P25451
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25451
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	J, X	198	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22141 Go to UniProtKB: P22141
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22141
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Reference Sequence

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| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-8,Proteasome subunit beta type-5	K, Y	211	Homo sapiens, Saccharomyces cerevisiae S288C This entity is chimeric	Mutation(s): 0 Gene Names: PSMB8, LMP7, PSMB5i, RING10, Y2, PRE2, DOA3, PRG1, YPR103W, P8283.10 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28062 (Homo sapiens) Explore P28062 Go to UniProtKB: P28062
PHAROS: P28062 GTEx: ENSG00000204264
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30656 Go to UniProtKB: P30656
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P30656 P28062
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6,Proteasome subunit beta type,Proteasome subunit beta type-6,Proteasome subunit beta type,Proteasome subunit beta type-6	L, Z	222	Saccharomyces cerevisiae S288C, Homo sapiens	Mutation(s): 0 Gene Names: PRE7, PRS3, PTS1, YBL041W, YBL0407 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P20618 (Homo sapiens) Explore P20618 Go to UniProtKB: P20618
PHAROS: P20618 GTEx: ENSG00000008018
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23724 Go to UniProtKB: P23724
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P23724 P20618
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	AA [auth a], M	246	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30657 Go to UniProtKB: P30657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P30657
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	BA [auth b], N	196	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P38624 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38624 Go to UniProtKB: P38624
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38624
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7DX Query on 7DX Download:Ideal Coordinates CCD File SDF format, chain MA [auth Y] SDF format, chain GA [auth K] MOL2 format, chain MA [auth Y] MOL2 format, chain GA [auth K] mmCIF format, chain MA [auth Y] mmCIF format, chain GA [auth K]	GA [auth K], MA [auth Y]	(2~{S})-2-cyclohexyl-4-oxidanylidene-4-[[7-(4-phenyl-1,3-thiazol-2-yl)quinolin-2-yl]amino]butanoic acid C₂₈ H₂₇ N₃ O₃ S APWRCWKBBYBSJJ-QFIPXVFZSA-N		Interactions Focus chain GA [auth K] Focus chain MA [auth Y] Interactions & Density Focus chain GA [auth K] Focus chain MA [auth Y]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain OA [auth b] SDF format, chain LA [auth U] SDF format, chain KA [auth N] SDF format, chain DA [auth G] MOL2 format, chain OA [auth b] MOL2 format, chain LA [auth U] MOL2 format, chain KA [auth N] MOL2 format, chain DA [auth G] mmCIF format, chain OA [auth b] mmCIF format, chain LA [auth U] mmCIF format, chain KA [auth N] mmCIF format, chain DA [auth G]	DA [auth G], KA [auth N], LA [auth U], OA [auth b]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain DA [auth G] Focus chain KA [auth N] Focus chain LA [auth U] Focus chain OA [auth b] Interactions & Density Focus chain DA [auth G] Focus chain KA [auth N] Focus chain LA [auth U] Focus chain OA [auth b]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain NA [auth Z] SDF format, chain JA [auth N] SDF format, chain IA [auth L] SDF format, chain HA [auth K] SDF format, chain FA [auth J] SDF format, chain EA [auth I] SDF format, chain CA [auth G] MOL2 format, chain NA [auth Z] MOL2 format, chain JA [auth N] MOL2 format, chain IA [auth L] MOL2 format, chain HA [auth K] MOL2 format, chain FA [auth J] MOL2 format, chain EA [auth I] MOL2 format, chain CA [auth G] mmCIF format, chain NA [auth Z] mmCIF format, chain JA [auth N] mmCIF format, chain IA [auth L] mmCIF format, chain HA [auth K] mmCIF format, chain FA [auth J] mmCIF format, chain EA [auth I] mmCIF format, chain CA [auth G]	CA [auth G] EA [auth I] FA [auth J] HA [auth K] IA [auth L] CA [auth G], EA [auth I], FA [auth J], HA [auth K], IA [auth L], JA [auth N], NA [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth G] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth N] Focus chain NA [auth Z] Interactions & Density Focus chain CA [auth G] Focus chain EA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain IA [auth L] Focus chain JA [auth N] Focus chain NA [auth Z]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.218 (Depositor), 0.221 (DCC)
R-Value Work: 0.200 (Depositor), 0.204 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.16	α = 90
b = 301.15	β = 112.81
c = 145.98	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-01-25

Deposition Author(s):

Groll, M.

Funding Organization	Location	Grant Number
German Research Foundation	Germany	GR1861/10-1

Revision History (Full details and data files)

Version 1.0: 2017-01-25
Type: Initial release
Version 1.1: 2017-03-29
Changes: Database references
Version 2.0: 2019-12-04
Changes: Atomic model, Author supporting evidence, Data collection, Source and taxonomy, Structure summary
Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

5M2B | pdb_00005m2b

Yeast 20S proteasome with human beta5i (1-138) and human beta6 (97-111; 118-133) in complex with thiazole based inhibitor Ro19

Literature

Structural Elucidation of a Nonpeptidic Inhibitor Specific for the Human Immunoproteasome.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)