9U7R | pdb_00009u7r

Substrate-free human 26S proteasome purified by midnolin, 20S proteasome, RPTs and RPN11 part

PDB DOI: https://doi.org/10.2210/pdb9U7R/pdb
EM Map EMD-63943: EMDB EMDataResource

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

Deposited: 2025-03-25 Released: 2026-04-01
Deposition Author(s): Zhu, C., Qin, L., Liang, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.17 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover

Zhu, C., Qin, L.

(2026) Nat Commun

DOI: https://doi.org/10.1038/s41467-026-71002-0

Macromolecule Content

Total Structure Weight: 1,085.31 kDa
Atom Count: 66,567
Modeled Residue Count: 8,618
Deposited Residue Count: 9,702
Unique protein chains: 21

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 14	A [auth c]	309	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O00487
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 7	B [auth A]	433	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P35998 (Homo sapiens) Explore P35998 Go to UniProtKB: P35998
PHAROS: P35998 GTEx: ENSG00000161057
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35998
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 4	C [auth B]	440	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62191 (Homo sapiens) Explore P62191 Go to UniProtKB: P62191
GTEx: ENSG00000100764
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62191
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 8	D [auth C]	398	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62195 (Homo sapiens) Explore P62195 Go to UniProtKB: P62195
PHAROS: P62195 GTEx: ENSG00000087191
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62195
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 6B	E [auth D]	418	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P43686 (Homo sapiens) Explore P43686 Go to UniProtKB: P43686
PHAROS: P43686 GTEx: ENSG00000013275
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43686
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome 26S subunit, ATPase 6	F [auth E]	403	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for A0A087X2I1 (Homo sapiens) Explore A0A087X2I1 Go to UniProtKB: A0A087X2I1
GTEx: ENSG00000100519
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A087X2I1
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome regulatory subunit 6A	G [auth F]	439	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P17980 (Homo sapiens) Explore P17980 Go to UniProtKB: P17980
PHAROS: P17980 GTEx: ENSG00000165916
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P17980
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-6	H [auth G], V [auth g]	245	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P60900 (Homo sapiens) Explore P60900 Go to UniProtKB: P60900
PHAROS: P60900 GTEx: ENSG00000100902
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60900
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-2	I [auth H], W [auth h]	233	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25787
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-4	J [auth I], X [auth i]	260	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25789
Sequence Annotations Expand
Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-7	K [auth J], Y [auth j]	247	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O14818
Sequence Annotations Expand
Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-5	L [auth K], Z [auth k]	240	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28066
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Long of Proteasome subunit alpha type-1	AA [auth l], M [auth L]	268	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25786 (Homo sapiens) Go to UniProtKB: P25786
PHAROS: P25786 GTEx: ENSG00000129084
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25786-2
Sequence Annotations Expand
Reference Sequence

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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit alpha type-3	BA [auth m], N [auth M]	254	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P25788 (Homo sapiens) Explore P25788 Go to UniProtKB: P25788
PHAROS: P25788 GTEx: ENSG00000100567
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P25788
Sequence Annotations Expand
Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-6	CA [auth n], O [auth N]	238	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28072 (Homo sapiens) Explore P28072 Go to UniProtKB: P28072
PHAROS: P28072 GTEx: ENSG00000142507
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28072
Sequence Annotations Expand
Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-7	DA [auth o], P [auth O]	276	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99436 (Homo sapiens) Explore Q99436 Go to UniProtKB: Q99436
PHAROS: Q99436 GTEx: ENSG00000136930
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99436
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-3	EA [auth p], Q [auth P]	204	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P49720 (Homo sapiens) Explore P49720 Go to UniProtKB: P49720
PHAROS: P49720 GTEx: ENSG00000277791
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49720
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-2	FA [auth q], R [auth Q]	201	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P49721 (Homo sapiens) Explore P49721 Go to UniProtKB: P49721
PHAROS: P49721 GTEx: ENSG00000126067
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49721
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-5	GA [auth r], S [auth R]	262	Homo sapiens	Mutation(s): 0 EC: 3.4.25.1
UniProt & NIH Common Fund Data Resources
Find proteins for P28074 (Homo sapiens) Explore P28074 Go to UniProtKB: P28074
PHAROS: P28074 GTEx: ENSG00000100804
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28074
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-1	HA [auth s], T [auth S]	240	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P20618 (Homo sapiens) Explore P20618 Go to UniProtKB: P20618
PHAROS: P20618 GTEx: ENSG00000008018
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P20618
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
Proteasome subunit beta type-4	IA [auth t], U [auth T]	263	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28070
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 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 KA [auth A] SDF format, chain MA [auth B] SDF format, chain PA [auth D] SDF format, chain QA [auth E] MOL2 format, chain KA [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth E] mmCIF format, chain KA [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain QA [auth E]	KA [auth A], MA [auth B], PA [auth D], QA [auth E]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain KA [auth A] Focus chain MA [auth B] Focus chain PA [auth D] Focus chain QA [auth E] Interactions & Density Focus chain KA [auth A] Focus chain MA [auth B] Focus chain PA [auth D] Focus chain QA [auth E]
LDZ (Subject of Investigation/LOI) Query on LDZ Download Ideal Coordinates CCD File SDF format, chain UA [auth N] SDF format, chain VA [auth O] SDF format, chain WA [auth R] SDF format, chain XA [auth n] SDF format, chain YA [auth o] SDF format, chain ZA [auth r] MOL2 format, chain UA [auth N] MOL2 format, chain VA [auth O] MOL2 format, chain WA [auth R] MOL2 format, chain XA [auth n] MOL2 format, chain YA [auth o] MOL2 format, chain ZA [auth r] mmCIF format, chain UA [auth N] mmCIF format, chain VA [auth O] mmCIF format, chain WA [auth R] mmCIF format, chain XA [auth n] mmCIF format, chain YA [auth o] mmCIF format, chain ZA [auth r]	UA [auth N] VA [auth O] WA [auth R] XA [auth n] YA [auth o] UA [auth N], VA [auth O], WA [auth R], XA [auth n], YA [auth o], ZA [auth r]	N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide C₂₆ H₄₁ N₃ O₅ TZYWCYJVHRLUCT-VABKMULXSA-N		Interactions Focus chain UA [auth N] Focus chain VA [auth O] Focus chain WA [auth R] Focus chain XA [auth n] Focus chain YA [auth o] Focus chain ZA [auth r] Interactions & Density Focus chain UA [auth N] Focus chain VA [auth O] Focus chain WA [auth R] Focus chain XA [auth n] Focus chain YA [auth o] Focus chain ZA [auth r]
ADP (Subject of Investigation/LOI) Query on ADP Download Ideal Coordinates CCD File SDF format, chain OA [auth C] SDF format, chain SA [auth F] MOL2 format, chain OA [auth C] MOL2 format, chain SA [auth F] mmCIF format, chain OA [auth C] mmCIF format, chain SA [auth F]	OA [auth C], SA [auth F]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain OA [auth C] Focus chain SA [auth F] Interactions & Density Focus chain OA [auth C] Focus chain SA [auth F]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain JA [auth c] MOL2 format, chain JA [auth c] mmCIF format, chain JA [auth c]	JA [auth c]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain JA [auth c] Interactions & Density Focus chain JA [auth c]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain LA [auth A] SDF format, chain NA [auth B] SDF format, chain RA [auth E] SDF format, chain TA [auth F] MOL2 format, chain LA [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain TA [auth F] mmCIF format, chain LA [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain RA [auth E] mmCIF format, chain TA [auth F]	LA [auth A], NA [auth B], RA [auth E], TA [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain LA [auth A] Focus chain NA [auth B] Focus chain RA [auth E] Focus chain TA [auth F] Interactions & Density Focus chain LA [auth A] Focus chain NA [auth B] Focus chain RA [auth E] Focus chain TA [auth F]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 26
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000907 (LDZ) Query on PRD_000907	UA [auth N] VA [auth O] WA [auth R] XA [auth n] YA [auth o] UA [auth N], VA [auth O], WA [auth R], XA [auth n], YA [auth o], ZA [auth r]	N-[(BENZYLOXY)CARBONYL]-L-LEUCYL-N-[(2S)-4-METHYL-1-OXOPENTAN-2-YL]-L-LEUCINAMIDE	Peptide-like / Inhibitor		Interactions Focus chain UA [auth N] Focus chain VA [auth O] Focus chain WA [auth R] Focus chain XA [auth n] Focus chain YA [auth o] Focus chain ZA [auth r] Interactions & Density Focus chain UA [auth N] Focus chain VA [auth O] Focus chain WA [auth R] Focus chain XA [auth n] Focus chain YA [auth o] Focus chain ZA [auth r]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.17 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2026-04-01

Deposition Author(s):

Zhu, C.

Qin, L.

Liang, L.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32171224

Revision History (Full details and data files)

Version 1.0: 2026-04-01
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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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; } 9U7R | pdb_00009u7r

Substrate-free human 26S proteasome purified by midnolin, 20S proteasome, RPTs and RPN11 part

Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover

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

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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

UniProt & NIH Common Fund Data Resources

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

Sequence Annotations

Entity ID: 14

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 19

9U7R | pdb_00009u7r