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
View more details

wwPDB Validation   3D Report Full Report


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


Literature

Structure of substrate engaged MIDN-bound human 26S proteasome, EB MIDN_UBL state

Peddada, N., Beutler, B.

To be published.

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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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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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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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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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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UniProt GroupP25787
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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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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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Find proteins for Q9UNM6 (Homo sapiens)
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GTEx:  ENSG00000185627 
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UniProt GroupQ9UNM6
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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
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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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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

View Full Validation Report



View more in-depth experimental data
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
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