8YJB | pdb_00008yjb

Cryo-EM structure of the human DSS1-INTAC complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

DSS1 is required for proper Integrator-PP2A function.

Xu, C.Zhou, Q.X.Zheng, H.Song, A.Zhao, W.Y.Xu, T.T.Xiong, Y.Zhang, Y.J.Huang, Z.Xu, Y.Cheng, J.Chen, F.X.

(2025) Nat Commun 16: 6206-6206

  • DOI: https://doi.org/10.1038/s41467-025-61257-4
  • Primary Citation of Related Structures:  
    8YJB, 9VD9

  • PubMed Abstract: 

    Integrator-PP2A (INTAC) is a highly modular complex orchestrating the transition of paused RNA polymerase II into productive elongation or promoter-proximal premature termination, with its loss resulting in transcription dysregulation and genome instability. Here, we identify human DSS1-a flexible 70-residue protein found in multiple functionally diverse complexes including the 26S proteasome-as an integral subunit of the INTAC backbone. Structural analysis of DSS1-INTAC, both alone and in association with paused polymerase, demonstrates intimate interactions between DSS1 and the INTAC backbone. We identify tryptophan 39 of DSS1 as being critical for interacting with INTAC and find that its mutation disrupts DSS1's interaction with INTAC, while maintaining DSS1's interaction with the proteasome. This substitution not only impairs INTAC-dependent transcriptional regulation, but also reveals that INTAC is DSS1's major chromatin-bound form. Together, our findings reveal a role for DSS1 in supporting the structure and regulatory functions of INTAC.


  • Organizational Affiliation
    • Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital, School of Life Sciences and Technology, Tongji University, Shanghai, China. conglingxu@tongji.edu.cn.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit DSS1A [auth 0]70Homo sapiensMutation(s): 0 
Gene Names: SHFM1DSS1SHFDG1
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GTEx:  ENSG00000127922 
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UniProt GroupP60896
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 9B [auth I]658Homo sapiensMutation(s): 0 
Gene Names: INTS9RC74
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GTEx:  ENSG00000104299 
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UniProt GroupQ9NV88
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 11C [auth K]600Homo sapiensMutation(s): 0 
Gene Names: INTS11CPSF3LRC68
EC: 3.1.27
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PHAROS:  Q5TA45
GTEx:  ENSG00000127054 
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UniProt GroupQ5TA45
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 2D [auth B]1,204Homo sapiensMutation(s): 0 
Gene Names: INTS2KIAA1287
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GTEx:  ENSG00000108506 
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UniProt GroupQ9H0H0
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 4E [auth D]963Homo sapiensMutation(s): 0 
Gene Names: INTS4MSTP093
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GTEx:  ENSG00000149262 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 7F [auth G]962Homo sapiensMutation(s): 0 
Gene Names: INTS7C1orf73
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GTEx:  ENSG00000143493 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoformG [auth P]589Homo sapiensMutation(s): 0 
Gene Names: PPP2R1A
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GTEx:  ENSG00000105568 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoformH [auth Q]309Homo sapiensMutation(s): 0 
Gene Names: PPP2CA
EC: 3.1.3.16
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GTEx:  ENSG00000113575 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 1I [auth A]2,190Homo sapiensMutation(s): 0 
Gene Names: INTS1KIAA1440UNQ1821/PRO3434
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GTEx:  ENSG00000164880 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 5J [auth E]1,019Homo sapiensMutation(s): 0 
Gene Names: INTS5KIAA1698
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GTEx:  ENSG00000185085 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 6K [auth F]887Homo sapiensMutation(s): 0 
Gene Names: INTS6DBI1DDX26DDX26A
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GTEx:  ENSG00000102786 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 8L [auth H]995Homo sapiensMutation(s): 0 
Gene Names: INTS8C8orf52
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GTEx:  ENSG00000164941 
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-05
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Data collection, Database references