9VD9 | pdb_00009vd9

Cryo-EM structure of the human DSS1-INTAC-PEC complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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:  
    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 SEM1A [auth 0]70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
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GTEx:  ENSG00000127922 
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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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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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GTEx:  ENSG00000127054 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 2E [auth B]1,204Homo sapiensMutation(s): 0 
Gene Names: INTS2KIAA1287
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GTEx:  ENSG00000108506 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 4F [auth D]963Homo sapiensMutation(s): 0 
Gene Names: INTS4MSTP093
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GTEx:  ENSG00000149262 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 7962Homo sapiensMutation(s): 0 
Gene Names: INTS7C1orf73
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GTEx:  ENSG00000143493 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1H [auth m]14Homo sapiensMutation(s): 0 
Gene Names: POLR2APOLR2
EC: 2.7.7.6 (PDB Primary Data), 3.1.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
THR-SER-PRO-SER-TYR-SER-PRO-THRI [auth n]8Homo sapiensMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoformJ [auth P]589Homo sapiensMutation(s): 0 
Gene Names: PPP2R1A
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GTEx:  ENSG00000105568 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoformK [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: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB1L [auth 1]1,970Homo sapiensMutation(s): 0 
Gene Names: POLR2APOLR2
EC: 2.7.7.6 (PDB Primary Data), 3.1.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta,DNA-directed RNA polymerase II subunit RPB2M [auth 2]1,300Sus scrofaHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6 (PDB Primary Data), 3.1.13 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3N [auth 3]275Homo sapiensMutation(s): 0 
Gene Names: POLR2CA-152E5.7
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GTEx:  ENSG00000102978 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1O [auth 4]210Homo sapiensMutation(s): 0 
Gene Names: POLR2E
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GTEx:  ENSG00000099817 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2P [auth 5]127Homo sapiensMutation(s): 0 
Gene Names: POLR2FPOLRF
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GTEx:  ENSG00000100142 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3Q [auth 6]150Homo sapiensMutation(s): 0 
Gene Names: POLR2H
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GTEx:  ENSG00000163882 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9R [auth 7]125Homo sapiensMutation(s): 0 
Gene Names: POLR2I
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GTEx:  ENSG00000105258 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5S [auth 8]67Homo sapiensMutation(s): 0 
Gene Names: POLR2L
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GTEx:  ENSG00000177700 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-aT [auth 9]117Homo sapiensMutation(s): 0 
Gene Names: POLR2JPOLR2J1
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GTEx:  ENSG00000005075 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4U [auth a]58Homo sapiensMutation(s): 0 
Gene Names: POLR2K
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GTEx:  ENSG00000147669 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor AX [auth e]528Homo sapiensMutation(s): 0 
Gene Names: NELFAWHSC2P/OKcl.15
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GTEx:  ENSG00000185049 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor BY [auth f]580Homo sapiensMutation(s): 0 
Gene Names: NELFBCOBRA1KIAA1182
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GTEx:  ENSG00000188986 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor C/DZ [auth g]590Homo sapiensMutation(s): 0 
Gene Names: NELFCDNELFDTH1TH1LHSPC130
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GTEx:  ENSG00000101158 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor EAA [auth h]22Homo sapiensMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4BA [auth i]117Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
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GTEx:  ENSG00000213246 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5CA [auth j]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7DA [auth k]172Homo sapiensMutation(s): 0 
Gene Names: POLR2GRPB7
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GTEx:  ENSG00000168002 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB4EA [auth l]142Homo sapiensMutation(s): 0 
Gene Names: POLR2D
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GTEx:  ENSG00000144231 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 1FA [auth A]2,190Homo sapiensMutation(s): 0 
Gene Names: INTS1KIAA1440UNQ1821/PRO3434
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GTEx:  ENSG00000164880 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 5GA [auth E]1,019Homo sapiensMutation(s): 0 
Gene Names: INTS5KIAA1698
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GTEx:  ENSG00000185085 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 6HA [auth F]887Homo sapiensMutation(s): 0 
Gene Names: INTS6DBI1DDX26DDX26A
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GTEx:  ENSG00000102786 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 8IA [auth H]995Homo sapiensMutation(s): 0 
Gene Names: INTS8C8orf52
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GTEx:  ENSG00000164941 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown2JA [auth M]17Homo sapiensMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
SER-PRO-THR-SERKA [auth p]4Homo sapiensMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
SER-PRO-LYS-TYR-SER-PRO-THR-SERLA [auth o]8Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains LengthOrganismImage
RNA (5'-R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)-3')D [auth c]21Homo sapiens
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Entity ID: 22
MoleculeChains LengthOrganismImage
DNA (48-MER)V [auth b]48Homo sapiens
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Entity ID: 23
MoleculeChains LengthOrganismImage
DNA (45-MER)W [auth d]45Homo sapiens
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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MA [auth K]
NA [auth K]
RA [auth 1]
SA [auth 1]
TA [auth 2]
MA [auth K],
NA [auth K],
RA [auth 1],
SA [auth 1],
TA [auth 2],
UA [auth 3],
VA [auth 7],
WA [auth 7],
XA [auth 8],
YA [auth a]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN
Query on MN

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OA [auth Q],
PA [auth Q]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG

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QA [auth 1]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-10-15
    Changes: Database references