9QB4 | pdb_00009qb4

Yeast 20S proteasome mutant: beta5_T3M in complex with Carfilzomib

PDB DOI: https://doi.org/10.2210/pdb9QB4/pdb

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

Deposited: 2025-02-28 Released: 2025-04-02
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: 2.70 Å
R-Value Free:
0.207 (Depositor), 0.211 (DCC)
R-Value Work:
0.173 (Depositor), 0.172 (DCC)
R-Value Observed:
0.175 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 2.0 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.

To be published.

Macromolecule Content

Total Structure Weight: 736.83 kDa
Atom Count: 49,952
Modelled Residue Count: 6,358
Deposited Residue Count: 6,640
Unique protein chains: 15

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	K, Y	211	Saccharomyces cerevisiae	Mutation(s): 1 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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by: Sequence | 3D Structure

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

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 NA [auth K] SDF format, chain KA [auth H] SDF format, chain SA [auth V] SDF format, chain WA [auth h] MOL2 format, chain NA [auth K] MOL2 format, chain KA [auth H] MOL2 format, chain SA [auth V] MOL2 format, chain WA [auth h] mmCIF format, chain NA [auth K] mmCIF format, chain KA [auth H] mmCIF format, chain SA [auth V] mmCIF format, chain WA [auth h]	KA [auth H], NA [auth K], SA [auth V], WA [auth h]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain KA [auth H] Focus chain NA [auth K] Focus chain SA [auth V] Focus chain WA [auth h] Interactions & Density Focus chain KA [auth H] Focus chain NA [auth K] Focus chain SA [auth V] Focus chain WA [auth h]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain JA [auth G] SDF format, chain PA [auth N] SDF format, chain QA [auth U] SDF format, chain VA [auth b] MOL2 format, chain JA [auth G] MOL2 format, chain PA [auth N] MOL2 format, chain QA [auth U] MOL2 format, chain VA [auth b] mmCIF format, chain JA [auth G] mmCIF format, chain PA [auth N] mmCIF format, chain QA [auth U] mmCIF format, chain VA [auth b]	JA [auth G], PA [auth N], QA [auth U], VA [auth b]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain JA [auth G] Focus chain PA [auth N] Focus chain QA [auth U] Focus chain VA [auth b] Interactions & Density Focus chain JA [auth G] Focus chain PA [auth N] Focus chain QA [auth U] Focus chain VA [auth b]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain IA [auth G] SDF format, chain LA [auth I] SDF format, chain MA [auth K] SDF format, chain OA [auth N] SDF format, chain RA [auth V] SDF format, chain TA [auth Y] SDF format, chain UA [auth Z] MOL2 format, chain IA [auth G] MOL2 format, chain LA [auth I] MOL2 format, chain MA [auth K] MOL2 format, chain OA [auth N] MOL2 format, chain RA [auth V] MOL2 format, chain TA [auth Y] MOL2 format, chain UA [auth Z] mmCIF format, chain IA [auth G] mmCIF format, chain LA [auth I] mmCIF format, chain MA [auth K] mmCIF format, chain OA [auth N] mmCIF format, chain RA [auth V] mmCIF format, chain TA [auth Y] mmCIF format, chain UA [auth Z]	IA [auth G] LA [auth I] MA [auth K] OA [auth N] RA [auth V] IA [auth G], LA [auth I], MA [auth K], OA [auth N], RA [auth V], TA [auth Y], UA [auth Z]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain IA [auth G] Focus chain LA [auth I] Focus chain MA [auth K] Focus chain OA [auth N] Focus chain RA [auth V] Focus chain TA [auth Y] Focus chain UA [auth Z] Interactions & Density Focus chain IA [auth G] Focus chain LA [auth I] Focus chain MA [auth K] Focus chain OA [auth N] Focus chain RA [auth V] Focus chain TA [auth Y] Focus chain UA [auth Z]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HPE Query on HPE	CA [auth e] DA [auth f] EA [auth g] FA [auth h] GA [auth i] CA [auth e], DA [auth f], EA [auth g], FA [auth h], GA [auth i], HA [auth j]	L-PEPTIDE LINKING	C₁₀ H₁₃ N O₂		PHE

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.207 (Depositor), 0.211 (DCC)
R-Value Work: 0.173 (Depositor), 0.172 (DCC)
R-Value Observed: 0.175 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.2	α = 90
b = 300.16	β = 112.84
c = 144.67	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-04-02

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: 2025-04-02
Type: Initial release
Version 2.0: 2025-04-09
Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary

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.

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left:-5px; } 9QB4 | pdb_00009qb4

Yeast 20S proteasome mutant: beta5_T3M in complex with Carfilzomib

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

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

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

UniProt

Entity Groups

Sequence Annotations

Entity ID: 15

Sequence Annotations

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9QB4 | pdb_00009qb4