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- PDB-8yjb: Cryo-EM structure of the human DSS1-INTAC complex -

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Entry
Database: PDB / ID: 8yjb
TitleCryo-EM structure of the human DSS1-INTAC complex
Components
  • (Integrator complex subunit ...) x 9
  • (Serine/threonine-protein phosphatase 2A ...) x 2
  • 26S proteasome complex subunit DSS1
KeywordsTRANSCRIPTION / DSS1 / Integrator / INTAC
Function / homology
Function and homology information


U2 snRNA 3'-end processing / snRNA 3'-end processing / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / regulation of hippo signaling / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / INTAC complex ...U2 snRNA 3'-end processing / snRNA 3'-end processing / PP2A-mediated dephosphorylation of key metabolic factors / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / regulation of hippo signaling / MASTL Facilitates Mitotic Progression / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / INTAC complex / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / FAR/SIN/STRIPAK complex / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / snRNA processing / regulation of growth / protein phosphatase regulator activity / protein antigen binding / GABA receptor binding / regulation of transcription elongation by RNA polymerase II / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / ERKs are inactivated / T cell homeostasis / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / Initiation of Nuclear Envelope (NE) Reformation / Co-stimulation by CD28 / integrator complex / RNA polymerase II transcription initiation surveillance / transcription export complex 2 / Disassembly of the destruction complex and recruitment of AXIN to the membrane / proteasome regulatory particle, lid subcomplex / protein dephosphorylation / negative regulation of glycolytic process through fructose-6-phosphate / negative regulation of epithelial to mesenchymal transition / Co-inhibition by CTLA4 / Platelet sensitization by LDL / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / cellular response to type I interferon / protein-serine/threonine phosphatase / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / ERK/MAPK targets / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / vascular endothelial cell response to oscillatory fluid shear stress / regulation of cell differentiation / protein serine/threonine phosphatase activity / Impaired BRCA2 binding to RAD51 / regulation of microtubule polymerization / RNA polymerase II transcribes snRNA genes / positive regulation of NLRP3 inflammasome complex assembly / chromosome, centromeric region / DARPP-32 events / lateral plasma membrane / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of hippo signaling / mRNA export from nucleus / proteasome assembly / Cyclin A/B1/B2 associated events during G2/M transition / DNA damage checkpoint signaling / spindle assembly / regulation of G1/S transition of mitotic cell cycle / phosphoprotein phosphatase activity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein localization to chromatin / RNA endonuclease activity / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / protein tyrosine phosphatase activity / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / proteasome complex / EML4 and NUDC in mitotic spindle formation / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / AURKA Activation by TPX2 / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of proteasomal protein catabolic process / Resolution of Sister Chromatid Cohesion / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / chromosome segregation / meiotic cell cycle / cellular response to ionizing radiation
Similarity search - Function
Domain of unknown function DUF3677 / Integrator complex subunit 2, metazoa / Integrator complex subunit 2 / Integrator complex subunit 7 / Integrator complex subunit 1 / : / : / : / : / : ...Domain of unknown function DUF3677 / Integrator complex subunit 2, metazoa / Integrator complex subunit 2 / Integrator complex subunit 7 / Integrator complex subunit 1 / : / : / : / : / : / : / Integrator complex subunit 1, RP2B-binding domain / Integrator complex subunit 2 / Integrator complex subunit 1, R3 domain / Integrator complex subunit 1, R4 domain / Integrator complex subunit 1, INTS2-binding domain / Integrator complex subunit 7, C-terminal domain / Integrator complex subunit 7, N-terminal / Integrator complex subunit 7 helical bundle / : / INTS6 beta-barrel domain / INTS6/SAGE1/DDX26B/CT45, C-terminal / : / INTS6/SAGE1/DDX26B/CT45 C-terminus / Integrator complex subunit 5, C-terminal / Integrator complex subunit 5, N-terminal / Integrator complex subunit 8 / Integrator complex subunit 5 / : / : / : / Integrator complex subunit 5 N-terminus / Integrator complex subunit 5 C-terminus / INTS8, TPR repeats / Integrator complex subunit 8, TPR repeats / Integrator complex subunit 8, TPR repeats / : / : / INTS4 8 helical bundle domain / Integrator subunit 4 family C-terminal Ig-like domain / Sister chromatid cohesion protein PDS5 protein / Integrator complex subunit 9 / : / Integrator IntS9, C-terminal domain / Integrator complex subunit 11, MBL-fold / : / Integrator IntS11, C-terminal domain / Metallo-beta-lactamase superfamily domain / : / Beta-Casp domain / : / : / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / : / PIK3R4-like, middle domain / HEAT repeat / HEAT repeat / : / PPP2R1A-like HEAT repeat / Serine/threonine specific protein phosphatases signature. / Protein phosphatase 2A homologues, catalytic domain. / Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase / DSS1/SEM1 / DSS1/SEM1 family / DSS1_SEM1 / von Willebrand factor type A domain / HEAT, type 2 / HEAT repeat profile. / HEAT repeats / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / VWFA domain profile. / von Willebrand factor, type A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / von Willebrand factor A-like domain superfamily / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
: / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / 26S proteasome complex subunit SEM1 / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Integrator complex subunit 11 / Integrator complex subunit 5 / Integrator complex subunit 8 / Integrator complex subunit 1 / Integrator complex subunit 4 / Integrator complex subunit 2 ...: / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / 26S proteasome complex subunit SEM1 / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Integrator complex subunit 11 / Integrator complex subunit 5 / Integrator complex subunit 8 / Integrator complex subunit 1 / Integrator complex subunit 4 / Integrator complex subunit 2 / Integrator complex subunit 9 / Integrator complex subunit 7 / Integrator complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsZheng, H. / Xu, Y. / Cheng, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2025
Title: DSS1 is required for proper Integrator-PP2A function.
Authors: Congling Xu / Qian-Xing Zhou / Hai Zheng / Aixia Song / Wen-Ying Zhao / Ting-Ting Xu / Yan Xiong / Yi-Jie Zhang / Zixuan Huang / Yanhui Xu / Jingdong Cheng / Fei Xavier Chen /
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 ...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.
History
DepositionMar 1, 2024Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
0: 26S proteasome complex subunit DSS1
I: Integrator complex subunit 9
K: Integrator complex subunit 11
B: Integrator complex subunit 2
D: Integrator complex subunit 4
G: Integrator complex subunit 7
P: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Q: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
A: Integrator complex subunit 1
E: Integrator complex subunit 5
F: Integrator complex subunit 6
H: Integrator complex subunit 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,167,33616
Polymers1,167,09512
Non-polymers2414
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 1 types, 1 molecules 0

#1: Protein 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot ...Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHFM1, DSS1, SHFDG1 / Production host: Homo sapiens (human) / References: UniProt: P60896

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Integrator complex subunit ... , 9 types, 9 molecules IKBDGAEFH

#2: Protein Integrator complex subunit 9 / Int9 / Protein related to CPSF subunits of 74 kDa / RC-74


Mass: 73891.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS9, RC74 / Production host: Homo sapiens (human) / References: UniProt: Q9NV88
#3: Protein Integrator complex subunit 11 / Int11 / Cleavage and polyadenylation-specific factor 3-like protein / CPSF3-like protein / Protein ...Int11 / Cleavage and polyadenylation-specific factor 3-like protein / CPSF3-like protein / Protein related to CPSF subunits of 68 kDa / RC-68


Mass: 67756.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS11, CPSF3L, RC68 / Production host: Homo sapiens (human)
References: UniProt: Q5TA45, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#4: Protein Integrator complex subunit 2 / Int2


Mass: 134451.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS2, KIAA1287 / Production host: Homo sapiens (human) / References: UniProt: Q9H0H0
#5: Protein Integrator complex subunit 4 / Int4


Mass: 108306.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS4, MSTP093 / Production host: Homo sapiens (human) / References: UniProt: Q96HW7
#6: Protein Integrator complex subunit 7 / Int7


Mass: 106952.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS7, C1orf73 / Production host: Homo sapiens (human) / References: UniProt: Q9NVH2
#9: Protein Integrator complex subunit 1 / Int1


Mass: 244574.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS1, KIAA1440, UNQ1821/PRO3434 / Production host: Homo sapiens (human) / References: UniProt: Q8N201
#10: Protein Integrator complex subunit 5 / Int5


Mass: 108115.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS5, KIAA1698 / Production host: Homo sapiens (human) / References: UniProt: Q6P9B9
#11: Protein Integrator complex subunit 6 / Int6 / DBI-1 / Protein DDX26 / Protein deleted in cancer 1 / DICE1


Mass: 100527.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS6, DBI1, DDX26, DDX26A / Production host: Homo sapiens (human) / References: UniProt: Q9UL03
#12: Protein Integrator complex subunit 8 / Int8 / Protein kaonashi-1


Mass: 113219.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS8, C8orf52 / Production host: Homo sapiens (human) / References: UniProt: Q75QN2

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Serine/threonine-protein phosphatase 2A ... , 2 types, 2 molecules PQ

#7: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Medium tumor antigen-associated 61 kDa protein / PP2A subunit A isoform PR65-alpha / PP2A subunit A ...Medium tumor antigen-associated 61 kDa protein / PP2A subunit A isoform PR65-alpha / PP2A subunit A isoform R1-alpha


Mass: 65378.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Production host: Homo sapiens (human) / References: UniProt: P30153
#8: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / PP2A-alpha / Replication protein C / RP-C


Mass: 35636.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Homo sapiens (human)
References: UniProt: P67775, protein-serine/threonine phosphatase

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Non-polymers , 2 types, 4 molecules

#13: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#14: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: DSS1-INTAC-PEC / Type: COMPLEX / Entity ID: #1-#12 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1Gautomatchparticle selection
2SerialEMimage acquisition
4RELIONCTF correction
7Cootmodel fitting
10RELIONinitial Euler assignment
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 587397
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 43790 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 7YCX

7ycx


Accession code: 7YCX / Source name: PDB / Type: experimental model

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