9BW4 | pdb_00009bw4

TXNL1-bound proteasome

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

  • Deposited: 2024-05-20 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, Richard and Susan Smith Family Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structure of the TXNL1-bound proteasome.

Gao, J., Nardone, C., Yip, M.C.J., Chino, H., Gu, X., Mirman, Z., Rale, M.J., Paulo, J.A., Elledge, S.J., Shao, S.

(2025) Nat Struct Mol Biol 32: 2398-2402

  • DOI: https://doi.org/10.1038/s41594-025-01639-w
  • Primary Citation of Related Structures:  
    9BW4

  • PubMed Abstract: 

    Proteasomes degrade diverse proteins in different cellular contexts through incompletely defined regulatory mechanisms. Here we report the cryo-EM structure of human thioredoxin-like protein 1 (TXNL1) bound to the 19S regulatory particle of proteasomes via interactions with PSMD1 (Rpn2), PSMD4 (Rpn10) and PSMD14 (Rpn11). Proteasome binding is necessary for the ubiquitin-independent degradation of TXNL1 upon cellular exposure to metal- or metalloid-containing oxidative agents, thereby establishing a structural requirement for the stress-induced degradation of TXNL1.

    • Organizational Affiliation: 
    • Department of Cell Biology, Harvard Medical School, Boston, MA, USA.

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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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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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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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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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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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 non-ATPase regulatory subunit 2L [auth f]908Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000175166 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-like protein 1M [auth x]289Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000091164 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7N [auth A]433Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000161057 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4O [auth B]440Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100764 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 8P [auth C]406Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000087191 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6BQ [auth D]418Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000013275 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S protease regulatory subunit 10BR [auth E]389Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100519 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6AS [auth F]439Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000165916 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-6T [auth G]246Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000100902 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-2U [auth H]234Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000106588 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-4V [auth I]261Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000041357 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-7W [auth J]248Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000101182 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Proteasome subunit alpha type-5X [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-1Y [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-3Z [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],
HA [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],
IA [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],
JA [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],
KA [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],
LA [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],
MA [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],
NA [auth t]		264Homo sapiensMutation(s): 0 
EC: 3.4.25.1
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GTEx:  ENSG00000159377 
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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]		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],
ZA [auth F]		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],
YA [auth E]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01AG073277
David and Lucile Packard FoundationUnited States2019-69660
Richard and Susan Smith Family FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-11
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Data collection, Database references
  • Version 1.2: 2025-12-24
    Changes: Data collection, Database references