9NKI | pdb_00009nki

Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state (Composite map)

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2025-02-28 Released: 2025-05-07 
  • Deposition Author(s): Peddada, N., Beutler, B.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9NKI

This is version 1.2 of the entry. See complete history

Literature

Structural insights into the ubiquitin-independent midnolin-proteasome pathway.

Peddada, N.Zhong, X.Yin, Y.Lazaro, D.R.Wang, J.Lyon, S.Choi, J.H.Bai, X.C.Moresco, E.M.Y.Beutler, B.

(2025) Proc Natl Acad Sci U S A 122: e2505345122-e2505345122

  • DOI: https://doi.org/10.1073/pnas.2505345122
  • Primary Citation Related Structures: 
    9NKF, 9NKG, 9NKI, 9NKJ

  • PubMed Abstract: 

    The protein midnolin (MIDN) augments proteasome activity in lymphocytes and dramatically facilitates the survival and proliferation of B-lymphoid malignancies. MIDN binds both to proteasomes and to substrates, but the mode of interaction with the proteasome is unknown, and the mechanism by which MIDN facilitates substrate degradation in a ubiquitin-independent manner is incompletely understood. Here, we present cryoelectron microscopy (cryo-EM) structures of the substrate-engaged, MIDN-bound human proteasome in two conformational states. MIDN induces proteasome conformations similarly to ubiquitinated substrates by using its ubiquitin-like domain to bind to the deubiquitinase RPN11 (PSMD14). By simultaneously binding to RPN1 (PSMD2) with its C-terminal α-helix, MIDN positions its substrate-carrying Catch domain above the proteasome ATPase channel through which substrates are translocated before degradation. Our findings suggest that both ubiquitin-like domain and C-terminal α-helix must bind to the proteasome for MIDN to stimulate proteasome activity.


  • Organizational Affiliation
    • Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX 75390.

Macromolecule Content 

  • Total Structure Weight: 1,717.71 kDa 
  • Atom Count: 102,622 
  • Modeled Residue Count: 13,398 
  • Deposited Residue Count: 15,364 
  • Unique protein chains: 34

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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UniProt GroupP35998
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4440Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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UniProt GroupP62191
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 8406Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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UniProt GroupP62195
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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UniProt GroupP43686
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 10B403Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6A439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6DA [auth g],
G
246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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UniProt GroupP60900
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2EA [auth h],
H
234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4FA [auth i],
I
261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7GA [auth j],
J
248Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000101182 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5HA [auth k],
K
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1IA [auth l],
L
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3JA [auth m],
M
255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6KA [auth n],
N
239Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7LA [auth o],
O
277Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3MA [auth p],
P
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2NA [auth q],
Q
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5OA [auth r],
R
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1PA [auth s],
S
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4QA [auth t],
T
264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3U [auth V]534Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108344 
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Entity ID: 22
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12V [auth W]456Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000197170 
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Entity ID: 23
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11W [auth X]422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108671 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6X [auth Y]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163636 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7Y [auth Z]324Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000103035 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13Z [auth a]376Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000185627 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4AA [auth b]377Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159352 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8BA [auth d]350Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099341 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1CA [auth e]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127922 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
Unknown density-substrate densityRA [auth v]12Homo sapiensMutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
MidnolinSA [auth z]468Homo sapiensMutation(s): 0 
Gene Names: MIDN
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GTEx:  ENSG00000167470 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1TA [auth U]953Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173692 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14UA [auth c]310Homo sapiensMutation(s): 0 
EC: 3.4.19 (PDB Primary Data), 3.4.19.12 (UniProt)
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GTEx:  ENSG00000115233 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2VA [auth f]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175166 
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
(Subject of Investigation/LOI)

Query on ATP



Download:Ideal Coordinates CCD File
BB [auth D],
DB [auth F],
WA [auth A],
YA [auth B]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
(Subject of Investigation/LOI)

Query on ADP



Download:Ideal Coordinates CCD File
CB [auth E]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
(Subject of Investigation/LOI)

Query on ZN



Download:Ideal Coordinates CCD File
FB [auth c]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
(Subject of Investigation/LOI)

Query on MG



Download:Ideal Coordinates CCD File
AB [auth D],
EB [auth F],
XA [auth A],
ZA [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286:
MODEL REFINEMENTCoot
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI125581
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA258602

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-21
    Changes: Data collection, Database references