9BV1 | pdb_00009bv1

M2A Midnolin-Proteasome (translocating)

  • Classification: NUCLEAR PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2024-05-19 Released: 2025-06-11 
  • Deposition Author(s): Gao, J., Yip, M.C.J., Shao, S.
  • Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA), David and Lucile Packard Foundation, Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 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 basis for nuclear protein degradation by the midnolin-proteasome pathway

Nardone, C.Gu, X.Gao, J.Yip, M.C.J.Seo, H.Song, K.Sebastian, L.Dhe-Paganon, S.Negasi, M.Kamitaki, N.Greenberg, M.E.Elledge, S.J.Shao, S.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1A [auth U]953Homo sapiensMutation(s): 0 
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Find proteins for Q99460 (Homo sapiens)
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GTEx:  ENSG00000173692 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3B [auth V]534Homo sapiensMutation(s): 0 
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Find proteins for O43242 (Homo sapiens)
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GTEx:  ENSG00000108344 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12C [auth W]456Homo sapiensMutation(s): 0 
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Find proteins for O00232 (Homo sapiens)
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PHAROS:  O00232
GTEx:  ENSG00000197170 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11D [auth X]422Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000108671 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6E [auth Y]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000163636 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7F [auth Z]324Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000103035 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13G [auth a]376Homo sapiensMutation(s): 0 
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Find proteins for Q9UNM6 (Homo sapiens)
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GTEx:  ENSG00000185627 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4H [auth b]377Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000159352 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14I [auth c]310Homo sapiensMutation(s): 0 
EC: 3.4.19
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GTEx:  ENSG00000115233 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8J [auth d]350Homo sapiensMutation(s): 0 
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Find proteins for P48556 (Homo sapiens)
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GTEx:  ENSG00000099341 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1K [auth e]70Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000127922 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7L [auth A]433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4M [auth B]440Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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UniProt GroupP62191
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 8N [auth C]406Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6BO [auth D]418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 10BP [auth E]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6AQ [auth F]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6R [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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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2S [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: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4T [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: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7U [auth J]248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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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: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5V [auth K]241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P28066 (Homo sapiens)
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GTEx:  ENSG00000143106 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-1W [auth L]263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P25786 (Homo sapiens)
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GTEx:  ENSG00000129084 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-3X [auth M]255Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100567 
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UniProt GroupP25788
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-6FA [auth n],
Y [auth N]
239Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000142507 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-7GA [auth o],
Z [auth O]
277Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for Q99436 (Homo sapiens)
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GTEx:  ENSG00000136930 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-3AA [auth P],
HA [auth p]
205Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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Find proteins for P49720 (Homo sapiens)
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GTEx:  ENSG00000277791 
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UniProt GroupP49720
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-2BA [auth Q],
IA [auth q]
201Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000126067 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-5CA [auth R],
JA [auth r]
263Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100804 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-1DA [auth S],
KA [auth s]
241Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000008018 
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UniProt GroupP20618
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit beta type-4EA [auth T],
LA [auth t]
264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2MA [auth f]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175166 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
MidnolinNA [auth y]505Homo sapiensMutation(s): 0 
Gene Names: MIDN
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Find proteins for Q504T8 (Homo sapiens)
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GTEx:  ENSG00000167470 
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
PA [auth A],
RA [auth B],
TA [auth C],
YA [auth F]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
VA [auth D],
XA [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
OA [auth c]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
QA [auth A],
SA [auth B],
UA [auth C],
WA [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01073277
David and Lucile Packard FoundationUnited States2019-69660
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release