9UG9 | pdb_00009ug9

The cryo-EM structure of 26S proteasome-Midnolin complex MB state

PDB DOI: https://doi.org/10.2210/pdb9UG9/pdb
EM Map EMD-64133: EMDB EMDataResource

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-04-11 Released: 2025-09-10
Deposition Author(s): Wang, H.Y., Xu, W.Q.
Funding Organization(s): National Natural Science Foundation of China (NSFC), Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure-based engineering of the midnolin-proteasome pathway for targeted protein degradation.

Wang, H., Zheng, Y., Wang, T., Zhang, X., Wang, P., Wei, C., Li, H., Wang, Q., Zhang, L., Ke, X., Xu, W.

(2026) Protein Cell 17: 83-88

PubMed: 40851512 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/procel/pwaf069
Primary Citation Related Structures:
9M2W, 9UF8, 9UG9

Organizational Affiliation

School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.

Macromolecule Content

Total Structure Weight: 1,718.87 kDa
Atom Count: 103,692
Modeled Residue Count: 13,463
Deposited Residue Count: 15,376
Unique protein chains: 34

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Midnolin	A [auth u]	491	Homo sapiens	Mutation(s): 0 Gene Names: MIDN
UniProt & NIH Common Fund Data Resources
Find proteins for Q504T8 (Homo sapiens) Explore Q504T8 Go to UniProtKB: Q504T8
PHAROS: Q504T8 GTEx: ENSG00000167470
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q504T8
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 8	B [auth d]	350	Homo sapiens	Mutation(s): 0
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Find proteins for P48556 (Homo sapiens) Explore P48556 Go to UniProtKB: P48556
PHAROS: P48556 GTEx: ENSG00000099341
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48556
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	C [auth m], GA [auth M]	255	Homo sapiens	Mutation(s): 0
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Find proteins for P25788 (Homo sapiens) Explore P25788 Go to UniProtKB: P25788
PHAROS: P25788 GTEx: ENSG00000100567
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25788
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	D [auth R], S [auth r]	263	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
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Find proteins for P28074 (Homo sapiens) Explore P28074 Go to UniProtKB: P28074
PHAROS: P28074 GTEx: ENSG00000100804
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28074
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	E [auth n], KA [auth N]	239	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
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Find proteins for P28072 (Homo sapiens) Explore P28072 Go to UniProtKB: P28072
PHAROS: P28072 GTEx: ENSG00000142507
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28072
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 10B	F [auth E]	389	Homo sapiens	Mutation(s): 0
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Find proteins for P62333 (Homo sapiens) Explore P62333 Go to UniProtKB: P62333
GTEx: ENSG00000100519
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62333
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 4	G [auth B]	440	Homo sapiens	Mutation(s): 0
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Find proteins for P62191 (Homo sapiens) Explore P62191 Go to UniProtKB: P62191
GTEx: ENSG00000100764
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62191
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome complex subunit SEM1	H [auth e]	70	Homo sapiens	Mutation(s): 0
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Find proteins for P60896 (Homo sapiens) Explore P60896 Go to UniProtKB: P60896
PHAROS: P60896 GTEx: ENSG00000127922
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60896
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	I [auth o], OA [auth O]	277	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
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Find proteins for Q99436 (Homo sapiens) Explore Q99436 Go to UniProtKB: Q99436
PHAROS: Q99436 GTEx: ENSG00000136930
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99436
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	J [auth S], U [auth s]	241	Homo sapiens	Mutation(s): 0
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Find proteins for P20618 (Homo sapiens) Explore P20618 Go to UniProtKB: P20618
PHAROS: P20618 GTEx: ENSG00000008018
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20618
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 6B	K [auth D]	418	Homo sapiens	Mutation(s): 0
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Find proteins for P43686 (Homo sapiens) Explore P43686 Go to UniProtKB: P43686
PHAROS: P43686 GTEx: ENSG00000013275
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P43686
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 6A	L [auth F]	439	Homo sapiens	Mutation(s): 0
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Find proteins for P17980 (Homo sapiens) Explore P17980 Go to UniProtKB: P17980
PHAROS: P17980 GTEx: ENSG00000165916
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17980
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	M [auth p], QA [auth P]	205	Homo sapiens	Mutation(s): 0
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Find proteins for P49720 (Homo sapiens) Explore P49720 Go to UniProtKB: P49720
PHAROS: P49720 GTEx: ENSG00000277791
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49720
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 1	N [auth U]	953	Homo sapiens	Mutation(s): 0
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Find proteins for Q99460 (Homo sapiens) Explore Q99460 Go to UniProtKB: Q99460
PHAROS: Q99460 GTEx: ENSG00000173692
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99460
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 8	O [auth C]	406	Homo sapiens	Mutation(s): 0
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Find proteins for P62195 (Homo sapiens) Explore P62195 Go to UniProtKB: P62195
PHAROS: P62195 GTEx: ENSG00000087191
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62195
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	CA [auth g], P [auth G]	246	Homo sapiens	Mutation(s): 0
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Find proteins for P60900 (Homo sapiens) Explore P60900 Go to UniProtKB: P60900
PHAROS: P60900 GTEx: ENSG00000100902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60900
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	Q [auth q], SA [auth Q]	201	Homo sapiens	Mutation(s): 0
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Find proteins for P49721 (Homo sapiens) Explore P49721 Go to UniProtKB: P49721
PHAROS: P49721 GTEx: ENSG00000126067
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49721
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 7	R [auth A]	433	Homo sapiens	Mutation(s): 0
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Find proteins for P35998 (Homo sapiens) Explore P35998 Go to UniProtKB: P35998
PHAROS: P35998 GTEx: ENSG00000161057
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35998
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 3	T [auth V]	534	Homo sapiens	Mutation(s): 0
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Find proteins for O43242 (Homo sapiens) Explore O43242 Go to UniProtKB: O43242
PHAROS: O43242 GTEx: ENSG00000108344
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O43242
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	V [auth T], Y [auth t]	264	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P28070 (Homo sapiens) Explore P28070 Go to UniProtKB: P28070
PHAROS: P28070 GTEx: ENSG00000159377
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28070
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Substrate	W [auth v]	15	Homo sapiens	Mutation(s): 0

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 12	X [auth W]	456	Homo sapiens	Mutation(s): 0
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Find proteins for O00232 (Homo sapiens) Explore O00232 Go to UniProtKB: O00232
PHAROS: O00232 GTEx: ENSG00000197170
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00232
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Reference Sequence

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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	EA [auth h], Z [auth H]	234	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25787 (Homo sapiens) Explore P25787 Go to UniProtKB: P25787
PHAROS: P25787 GTEx: ENSG00000106588
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25787
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 2	AA [auth f]	908	Homo sapiens	Mutation(s): 0
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Find proteins for Q13200 (Homo sapiens) Explore Q13200 Go to UniProtKB: Q13200
PHAROS: Q13200 GTEx: ENSG00000175166
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13200
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 11	BA [auth X]	422	Homo sapiens	Mutation(s): 0
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Find proteins for O00231 (Homo sapiens) Explore O00231 Go to UniProtKB: O00231
PHAROS: O00231 GTEx: ENSG00000108671
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00231
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	DA [auth I], IA [auth i]	261	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25789 (Homo sapiens) Explore P25789 Go to UniProtKB: P25789
PHAROS: P25789 GTEx: ENSG00000041357
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25789
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 6	FA [auth Y]	389	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15008 (Homo sapiens) Explore Q15008 Go to UniProtKB: Q15008
PHAROS: Q15008 GTEx: ENSG00000163636
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15008
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-7	HA [auth J], MA [auth j]	248	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O14818 (Homo sapiens) Explore O14818 Go to UniProtKB: O14818
PHAROS: O14818 GTEx: ENSG00000101182
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O14818
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 7	JA [auth Z]	324	Homo sapiens	Mutation(s): 0
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Find proteins for P51665 (Homo sapiens) Explore P51665 Go to UniProtKB: P51665
PHAROS: P51665 GTEx: ENSG00000103035
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UniProt Group	P51665
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	LA [auth K], TA [auth k]	241	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P28066 (Homo sapiens) Explore P28066 Go to UniProtKB: P28066
PHAROS: P28066 GTEx: ENSG00000143106
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P28066
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Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 13	NA [auth a]	376	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNM6 (Homo sapiens) Explore Q9UNM6 Go to UniProtKB: Q9UNM6
PHAROS: Q9UNM6 GTEx: ENSG00000185627
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UNM6
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-1	PA [auth L], VA [auth l]	263	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens) Explore P25786 Go to UniProtKB: P25786
PHAROS: P25786 GTEx: ENSG00000129084
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25786
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 4	RA [auth b]	377	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P55036 (Homo sapiens) Explore P55036 Go to UniProtKB: P55036
PHAROS: P55036 GTEx: ENSG00000159352
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55036
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 14	UA [auth c]	310	Homo sapiens	Mutation(s): 0 EC: 3.4.19 (PDB Primary Data), 3.4.19.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O00487 (Homo sapiens) Explore O00487 Go to UniProtKB: O00487
PHAROS: O00487 GTEx: ENSG00000115233
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O00487
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain YA [auth D] SDF format, chain ZA [auth F] MOL2 format, chain AB [auth A] MOL2 format, chain YA [auth D] MOL2 format, chain ZA [auth F] mmCIF format, chain AB [auth A] mmCIF format, chain YA [auth D] mmCIF format, chain ZA [auth F]	AB [auth A], YA [auth D], ZA [auth F]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain AB [auth A] Focus chain YA [auth D] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth A] Focus chain YA [auth D] Focus chain ZA [auth F]
ADP (Subject of Investigation/LOI) Query on ADP Download:Ideal Coordinates CCD File SDF format, chain WA [auth E] SDF format, chain XA [auth B] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth B] mmCIF format, chain WA [auth E] mmCIF format, chain XA [auth B]	WA [auth E], XA [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain WA [auth E] Focus chain XA [auth B] Interactions & Density Focus chain WA [auth E] Focus chain XA [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain BB [auth c] MOL2 format, chain BB [auth c] mmCIF format, chain BB [auth c]	BB [auth c]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BB [auth c] Interactions & Density Focus chain BB [auth c]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-09-10

Deposition Author(s):

Wang, H.Y.

Xu, W.Q.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32000862
Other government		BX20200351
Other government		24ZR1451800
Other government		2021kf01

Revision History (Full details and data files)

Version 1.0: 2025-09-10
Type: Initial release
Version 1.1: 2026-07-01
Changes: Data collection, Database references

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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.

9UG9 | pdb_00009ug9

The cryo-EM structure of 26S proteasome-Midnolin complex MB state

Literature

Structure-based engineering of the midnolin-proteasome pathway for targeted protein degradation.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 3

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Entity Groups

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Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 7

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 10

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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 & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 14

UniProt & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 15

UniProt & NIH Common Fund Data Resources

Entity Groups

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Entity ID: 16

UniProt & NIH Common Fund Data Resources

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Entity ID: 17

UniProt & NIH Common Fund Data Resources

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Entity ID: 18

UniProt & NIH Common Fund Data Resources

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Entity ID: 19

UniProt & NIH Common Fund Data Resources