9QBY | pdb_00009qby

Yeast 20S proteasome mutant: beta5_G128V (b5-propeptide in trans) in complex with ONX0914

PDB DOI: https://doi.org/10.2210/pdb9QBY/pdb

Classification: HYDROLASE
Organism(s): Saccharomyces cerevisiae, synthetic construct
Expression System: Saccharomyces cerevisiae
Mutation(s): Yes

Deposited: 2025-03-04 Released: 2025-10-08
Deposition Author(s): Huber, E.M., Heinemeyer, W., Groll, M.
Funding Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.211 (Depositor), 0.214 (DCC)
R-Value Work:
0.177 (Depositor), 0.157 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Proteasome-associated autoinflammatory syndromes: The impact of mutations in proteasome subunits on particle assembly, structure, and activity

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

(2025) Structure

DOI: https://doi.org/10.1016/j.str.2025.09.004

Macromolecule Content

Total Structure Weight: 736.18 kDa
Atom Count: 49,907
Modeled Residue Count: 6,361
Deposited Residue Count: 6,632
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
Entity Groups
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
Entity Groups
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
Entity Groups
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): 1 Gene Names: PRE2, DOA3, PRG1, YPR103W, P8283.10 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	195	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
3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE	CA [auth d] DA [auth e] EA [auth f] FA [auth g] GA [auth h] CA [auth d], DA [auth e], EA [auth f], FA [auth g], GA [auth h], HA [auth i]	4	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain KA [auth G] SDF format, chain LA [auth H] SDF format, chain NA [auth M] SDF format, chain QA [auth U] SDF format, chain RA [auth V] SDF format, chain TA [auth a] MOL2 format, chain KA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain NA [auth M] MOL2 format, chain QA [auth U] MOL2 format, chain RA [auth V] MOL2 format, chain TA [auth a] mmCIF format, chain KA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain NA [auth M] mmCIF format, chain QA [auth U] mmCIF format, chain RA [auth V] mmCIF format, chain TA [auth a]	KA [auth G] LA [auth H] NA [auth M] QA [auth U] RA [auth V] KA [auth G], LA [auth H], NA [auth M], QA [auth U], RA [auth V], TA [auth a]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain KA [auth G] Focus chain LA [auth H] Focus chain NA [auth M] Focus chain QA [auth U] Focus chain RA [auth V] Focus chain TA [auth a] Interactions & Density Focus chain KA [auth G] Focus chain LA [auth H] Focus chain NA [auth M] Focus chain QA [auth U] Focus chain RA [auth V] Focus chain TA [auth a]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain MA [auth K] SDF format, chain UA [auth a] MOL2 format, chain MA [auth K] MOL2 format, chain UA [auth a] mmCIF format, chain MA [auth K] mmCIF format, chain UA [auth a]	MA [auth K], UA [auth a]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain MA [auth K] Focus chain UA [auth a] Interactions & Density Focus chain MA [auth K] Focus chain UA [auth a]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain JA [auth G] SDF format, chain PA [auth U] MOL2 format, chain JA [auth G] MOL2 format, chain PA [auth U] mmCIF format, chain JA [auth G] mmCIF format, chain PA [auth U]	JA [auth G], PA [auth U]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain JA [auth G] Focus chain PA [auth U] Interactions & Density Focus chain JA [auth G] Focus chain PA [auth U]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain IA [auth G] SDF format, chain OA [auth N] SDF format, chain SA [auth W] MOL2 format, chain IA [auth G] MOL2 format, chain OA [auth N] MOL2 format, chain SA [auth W] mmCIF format, chain IA [auth G] mmCIF format, chain OA [auth N] mmCIF format, chain SA [auth W]	IA [auth G], OA [auth N], SA [auth W]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain IA [auth G] Focus chain OA [auth N] Focus chain SA [auth W] Interactions & Density Focus chain IA [auth G] Focus chain OA [auth N] Focus chain SA [auth W]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
0A1 Query on 0A1	CA [auth d] DA [auth e] EA [auth f] FA [auth g] GA [auth h] CA [auth d], DA [auth e], EA [auth f], FA [auth g], GA [auth h], HA [auth i]	L-PEPTIDE LINKING	C₁₀ H₁₃ N O₃		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.211 (Depositor), 0.214 (DCC)
R-Value Work: 0.177 (Depositor), 0.157 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 136.44	α = 90
b = 300.23	β = 113.3
c = 146.21	γ = 90

Software Package:

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

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-10-08

Deposition Author(s):

Huber, E.M.

Heinemeyer, W.

Groll, M.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	SFB1035, project no.201302640, A02

Revision History (Full details and data files)

Version 1.0: 2025-10-08
Type: Initial release

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.

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 9QBY | pdb_00009qby

Yeast 20S proteasome mutant: beta5_G128V (b5-propeptide in trans) in complex with ONX0914

Proteasome-associated autoinflammatory syndromes: The impact of mutations in proteasome subunits on particle assembly, structure, and activity

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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Sequence Annotations

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Entity ID: 11

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Entity ID: 12

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Entity ID: 13

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Entity ID: 14

UniProt

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Entity ID: 15

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9QBY | pdb_00009qby