9NKJ | pdb_00009nkj

Structure of substrates-engaged MIDN-bound human 26S proteasome,ED-MIDN state (Composite map)

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • 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: 3.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7433Homo sapiensMutation(s): 0 
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Find proteins for P35998 (Homo sapiens)
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GTEx:  ENSG00000161057 
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UniProt GroupP35998
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4440Homo sapiensMutation(s): 0 
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Find proteins for P62191 (Homo sapiens)
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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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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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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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UniProt GroupA0A087X2I1
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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
26S proteasome non-ATPase regulatory subunit 1G [auth U]953Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000173692 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3H [auth V]534Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108344 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11I [auth X]422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108671 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6J [auth Y]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163636 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7K [auth Z]324Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000103035 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13L [auth a]376Homo sapiensMutation(s): 0 
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Find proteins for Q9UNM6 (Homo sapiens)
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PHAROS:  Q9UNM6
GTEx:  ENSG00000185627 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4M [auth b]377Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159352 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14N [auth c]310Homo sapiensMutation(s): 0 
EC: 3.4.19
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GTEx:  ENSG00000115233 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8O [auth d]350Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000099341 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2P [auth f]908Homo sapiensMutation(s): 0 
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Find proteins for Q13200 (Homo sapiens)
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GTEx:  ENSG00000175166 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
unknown density-Substrate densityQ [auth v]8Homo sapiensMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12R [auth W]456Homo sapiensMutation(s): 0 
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Find proteins for O00232 (Homo sapiens)
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GTEx:  ENSG00000197170 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1S [auth e]70Homo sapiensMutation(s): 0 
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Find proteins for P60896 (Homo sapiens)
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GTEx:  ENSG00000127922 
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UniProt GroupP60896
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6HA [auth g],
T [auth G]		246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P60900 (Homo sapiens)
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GTEx:  ENSG00000100902 
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UniProt GroupP60900
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2IA [auth h],
U [auth H]		234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P25787 (Homo sapiens)
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GTEx:  ENSG00000106588 
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UniProt GroupP25787
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4JA [auth i],
V [auth I]		261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P25789 (Homo sapiens)
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GTEx:  ENSG00000041357 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7KA [auth j],
W [auth J]		248Homo sapiensMutation(s): 0 
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Find proteins for O14818 (Homo sapiens)
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GTEx:  ENSG00000101182 
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UniProt GroupO14818
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5LA [auth k],
X [auth K]		241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000143106 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1MA [auth l],
Y [auth L]		263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000129084 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3NA [auth m],
Z [auth M]		255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6AA [auth N],
OA [auth n]		239Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7BA [auth O],
PA [auth o]		277Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000136930 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3CA [auth P],
QA [auth p]		205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000277791 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2DA [auth Q],
RA [auth q]		201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5EA [auth R],
SA [auth r]		263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1FA [auth S],
TA [auth s]		241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4GA [auth T],
UA [auth t]		264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP
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BB [auth F],
VA [auth A],
XA [auth B],
ZA [auth C]		ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
LDZ (Subject of Investigation/LOI)
Query on LDZ
Download Ideal Coordinates CCD File 
EB [auth N]
FB [auth O]
GB [auth R]
HB [auth n]
IB [auth o]
EB [auth N],
FB [auth O],
GB [auth R],
HB [auth n],
IB [auth o],
JB [auth r]
N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide
C26 H41 N3 O5
TZYWCYJVHRLUCT-VABKMULXSA-N
ADP (Subject of Investigation/LOI)
Query on ADP
Download Ideal Coordinates CCD File 
AB [auth D]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
DB [auth c]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG
Download Ideal Coordinates CCD File 
CB [auth F],
WA [auth A],
YA [auth B]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX1.21.1_5286:
MODEL REFINEMENTCoot

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