9S78 | pdb_00009s78

Yeast 20S Proteasome in Complex with Tellurophene-Tagged Carfilzomib

PDB DOI: https://doi.org/10.2210/pdb9S78/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae, synthetic construct
Mutation(s): No

Deposited: 2025-08-04 Released: 2025-12-24
Deposition Author(s): Potter, N., Eddenden, A., Fomina, A., Dinesh, A., Jackson, H.W., McGuigan, A., Groll, M., Nitz, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.15 Å
R-Value Free:
0.223 (Depositor), 0.229 (DCC)
R-Value Work:
0.185 (Depositor), 0.196 (DCC)
R-Value Observed:
0.187 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Tellurophene-Tagged Carfilzomib Enables Single-Cell Mass Cytometric Mapping of Proteasome Activity.

Potter, N., Eddenden, A., Fomina, A., Dinesh, A., Jackson, H.W., McGuigan, A.P., Groll, M., Nitz, M.

(2025) ACS Chem Biol

PubMed: 41252648 Search on PubMed
DOI: https://doi.org/10.1021/acschembio.5c00691
Primary Citation of Related Structures:
9S78

PubMed Abstract:
Tracking small-molecule distribution in heterogeneous cell samples at single-cell resolution remains a major analytical challenge. Here, we present a tellurophene-functionalized analogue of the proteasome inhibitor Carfilzomib (TeCar) whose distribution can be followed by mass cytometric (MC) quantification while preserving target engagement and cytotoxicity. Structural and biochemical analyses confirm that TeCar binds the proteasome in a mode comparable to the clinically approved parent compound. Using MC, we demonstrate selective TeCar accumulation in malignant over immune cells within mixed populations, with cancer cells exhibiting 15 to 30-fold higher uptake. Tellurium signal correlates with proteasomal activity, and differential labeling among immune subsets reveals functional heterogeneity not captured by transcriptomics alone. These findings establish tellurophene tagging as a minimally perturbing and broadly applicable strategy for functional distribution studies at single-cell resolution.

Organizational Affiliation

Department of Chemistry, University of Toronto, Toronto M5S3H6, Canada.

Macromolecule Content

Total Structure Weight: 735.5 kDa
Atom Count: 49,638
Modeled Residue Count: 6,351
Deposited Residue Count: 6,630
Unique protein chains: 15

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	A, O	250	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23639 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23639 Go to UniProtKB: P23639
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23639
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	B, P	258	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23638 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23638 Go to UniProtKB: P23638
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23638
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	C, Q	254	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40303 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40303 Go to UniProtKB: P40303
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40303
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	D, R	260	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P32379 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P32379 Go to UniProtKB: P32379
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P32379
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	E, S	234	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P40302 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40302 Go to UniProtKB: P40302
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40302
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable proteasome subunit alpha type-7	F, T	288	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P21242 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21242 Go to UniProtKB: P21242
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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	Mutation(s): 0
UniProt
Find proteins for P21243 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P21243 Go to UniProtKB: P21243
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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	231	Saccharomyces cerevisiae	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
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25043
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	I, W	205	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P25451 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25451 Go to UniProtKB: P25451
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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	Mutation(s): 0
UniProt
Find proteins for P22141 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22141 Go to UniProtKB: P22141
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22141
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	K, Y	211	Saccharomyces cerevisiae	Mutation(s): 0 EC: 3.4.25.1
UniProt
Find proteins for P30656 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30656 Go to UniProtKB: P30656
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30656
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	L, Z	222	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P23724 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P23724 Go to UniProtKB: P23724
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23724
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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	Mutation(s): 0
UniProt
Find proteins for P30657 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P30657 Go to UniProtKB: P30657
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% 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	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P38624
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Carfilzomib (Tellurophene-Tagged)	CA [auth e], DA [auth f], EA [auth g], FA [auth h]	5	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain IA [auth H] SDF format, chain PA [auth V] SDF format, chain TA [auth f] SDF format, chain UA [auth h] MOL2 format, chain IA [auth H] MOL2 format, chain PA [auth V] MOL2 format, chain TA [auth f] MOL2 format, chain UA [auth h] mmCIF format, chain IA [auth H] mmCIF format, chain PA [auth V] mmCIF format, chain TA [auth f] mmCIF format, chain UA [auth h]	IA [auth H], PA [auth V], TA [auth f], UA [auth h]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain IA [auth H] Focus chain PA [auth V] Focus chain TA [auth f] Focus chain UA [auth h] Interactions & Density Focus chain IA [auth H] Focus chain PA [auth V] Focus chain TA [auth f] Focus chain UA [auth h]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain HA [auth G] SDF format, chain MA [auth N] SDF format, chain NA [auth U] SDF format, chain SA [auth b] MOL2 format, chain HA [auth G] MOL2 format, chain MA [auth N] MOL2 format, chain NA [auth U] MOL2 format, chain SA [auth b] mmCIF format, chain HA [auth G] mmCIF format, chain MA [auth N] mmCIF format, chain NA [auth U] mmCIF format, chain SA [auth b]	HA [auth G], MA [auth N], NA [auth U], SA [auth b]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain HA [auth G] Focus chain MA [auth N] Focus chain NA [auth U] Focus chain SA [auth b] Interactions & Density Focus chain HA [auth G] Focus chain MA [auth N] Focus chain NA [auth U] Focus chain SA [auth b]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain GA [auth G] SDF format, chain JA [auth I] SDF format, chain KA [auth K] SDF format, chain LA [auth N] SDF format, chain OA [auth V] SDF format, chain QA [auth Y] SDF format, chain RA [auth Z] MOL2 format, chain GA [auth G] MOL2 format, chain JA [auth I] MOL2 format, chain KA [auth K] MOL2 format, chain LA [auth N] MOL2 format, chain OA [auth V] MOL2 format, chain QA [auth Y] MOL2 format, chain RA [auth Z] mmCIF format, chain GA [auth G] mmCIF format, chain JA [auth I] mmCIF format, chain KA [auth K] mmCIF format, chain LA [auth N] mmCIF format, chain OA [auth V] mmCIF format, chain QA [auth Y] mmCIF format, chain RA [auth Z]	GA [auth G] JA [auth I] KA [auth K] LA [auth N] OA [auth V] GA [auth G], JA [auth I], KA [auth K], LA [auth N], OA [auth V], QA [auth Y], RA [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GA [auth G] Focus chain JA [auth I] Focus chain KA [auth K] Focus chain LA [auth N] Focus chain OA [auth V] Focus chain QA [auth Y] Focus chain RA [auth Z] Interactions & Density Focus chain GA [auth G] Focus chain JA [auth I] Focus chain KA [auth K] Focus chain LA [auth N] Focus chain OA [auth V] Focus chain QA [auth Y] Focus chain RA [auth Z]