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- PDB-8rbz: Structure of Integrator-PP2A-SOSS-CTD post-termination complex -

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Entry
Database: PDB / ID: 8rbz
TitleStructure of Integrator-PP2A-SOSS-CTD post-termination complex
Components
  • (Integrator complex subunit ...) x 14
  • (SOSS complex subunit ...) x 2
  • (Serine/threonine-protein phosphatase 2A ...) x 2
  • DNA-directed RNA polymerase subunit
  • DSS1
  • UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
KeywordsTRANSCRIPTION / Integrator complex / Post-termination complex / RNA Polymerase II / Pol II / RNAPII
Function / homology
Function and homology information


SOSS complex / U2 snRNA 3'-end processing / regulation of fertilization / INTAC complex / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / snRNA 3'-end processing / RNA polymerase II transcription initiation surveillance / MASTL Facilitates Mitotic Progression ...SOSS complex / U2 snRNA 3'-end processing / regulation of fertilization / INTAC complex / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / snRNA 3'-end processing / RNA polymerase II transcription initiation surveillance / MASTL Facilitates Mitotic Progression / mitotic sister chromatid separation / protein phosphatase type 2A complex / establishment of protein localization to telomere / protein serine/threonine phosphatase complex / regulation of meiotic cell cycle process involved in oocyte maturation / peptidyl-threonine dephosphorylation / meiotic sister chromatid cohesion, centromeric / snRNA processing / peptidyl-serine dephosphorylation / protein localization to nuclear envelope / FAR/SIN/STRIPAK complex / : / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / histone H2AXS139 phosphatase activity / RNA polymerase II CTD heptapeptide repeat Y1 phosphatase activity / RNA polymerase II CTD heptapeptide repeat T4 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S2 phosphatase activity / RNA polymerase II CTD heptapeptide repeat S7 phosphatase activity / MAP kinase serine/threonine phosphatase activity / female meiotic nuclear division / myosin phosphatase activity / eye development / regulation of transcription elongation by RNA polymerase II / protein phosphatase regulator activity / calmodulin-dependent protein phosphatase activity / RNA polymerase II CTD heptapeptide repeat S5 phosphatase activity / flagellated sperm motility / GABA receptor binding / integrator complex / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / protein antigen binding / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / G-rich strand telomeric DNA binding / positive regulation of telomere capping / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / mRNA Splicing - Major Pathway / ERKs are inactivated / Initiation of Nuclear Envelope (NE) Reformation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / mitotic G2/M transition checkpoint / Co-stimulation by CD28 / regulation of growth / Disassembly of the destruction complex and recruitment of AXIN to the membrane / centrosome localization / negative regulation of epithelial to mesenchymal transition / inner cell mass cell proliferation / Co-inhibition by CTLA4 / response to ionizing radiation / Platelet sensitization by LDL / protein-serine/threonine phosphatase / negative regulation of glycolytic process through fructose-6-phosphate / positive regulation of NLRP3 inflammasome complex assembly / ERK/MAPK targets / protein serine/threonine phosphatase activity / mesoderm development / vascular endothelial cell response to oscillatory fluid shear stress / T cell homeostasis / regulation of G1/S transition of mitotic cell cycle / regulation of cell differentiation / phosphoprotein phosphatase activity / RNA polymerase II transcribes snRNA genes / chromosome, centromeric region
Similarity search - Function
SOSS complex subunit C / SOSS complex subunit C / Integrator complex subunit 3, N-terminal / Integrator complex subunit 3 / : / Integrator complex subunit 3 N-terminal / Ints3-like, C-terminal HEAT repeats / : / Single-stranded DNA binding protein Ssb-like, OB fold / Domain of unknown function DUF3677 ...SOSS complex subunit C / SOSS complex subunit C / Integrator complex subunit 3, N-terminal / Integrator complex subunit 3 / : / Integrator complex subunit 3 N-terminal / Ints3-like, C-terminal HEAT repeats / : / Single-stranded DNA binding protein Ssb-like, OB fold / Domain of unknown function DUF3677 / Integrator complex subunit 10 / Integrator complex subunit 2, metazoa / Integrator complex subunit 15 / Integrator complex subunit 2 / Integrator complex subunit 7 / Integrator complex subunit 1 / Integrator complex subunit 14 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, C-terminal / : / : / : / : / : / : / Integrator complex subunit 1, RP2B-binding domain / Integrator complex subunit 2 / Integrator complex subunit 15 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, alpha-helical domain / Integrator subunit 10 / 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 / Cell cycle regulator Mat89Bb / Cell cycle and development regulator Mat89Bb / 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 / : / 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 / 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 / HEAT repeat profile. / HEAT, type 2 / von Willebrand factor type A domain / HEAT repeats / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / Metallo-dependent phosphatase-like / RNA polymerase Rpb1 C-terminal repeat / RNA polymerase II, heptapeptide repeat, eukaryotic / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / VWFA domain profile. / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / von Willebrand factor, type A / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / von Willebrand factor A-like domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily
Similarity search - Domain/homology
: / DNA-directed RNA polymerase subunit / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Integrator complex subunit 11 / Integrator complex subunit 3 / Integrator complex subunit 5 / Integrator complex subunit 8 / Integrator complex subunit 1 / Integrator complex subunit 4 ...: / DNA-directed RNA polymerase subunit / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Integrator complex subunit 11 / Integrator complex subunit 3 / Integrator complex subunit 5 / Integrator complex subunit 8 / Integrator complex subunit 1 / Integrator complex subunit 4 / Integrator complex subunit 15 / Integrator complex subunit 14 / SOSS complex subunit B1 / Integrator complex subunit 2 / SOSS complex subunit C / Integrator complex subunit 9 / Integrator complex subunit 7 / Integrator complex subunit 13 / Integrator complex subunit 10 / Integrator complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
Trichoplusia ni (cabbage looper)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsFianu, I. / Ochmann, M. / Walshe, J.L. / Cramer, P.
Funding support Germany, European Union, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)SFB1565 Germany
European Research Council (ERC)EXC 2067/1-390729940European Union
CitationJournal: Nature / Year: 2024
Title: Structural basis of Integrator-dependent RNA polymerase II termination.
Authors: Isaac Fianu / Moritz Ochmann / James L Walshe / Olexandr Dybkov / Joseph Neos Cruz / Henning Urlaub / Patrick Cramer /
Abstract: The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex ...The Integrator complex can terminate RNA polymerase II (Pol II) in the promoter-proximal region of genes. Previous work has shed light on how Integrator binds to the paused elongation complex consisting of Pol II, the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) and how it cleaves the nascent RNA transcript, but has not explained how Integrator removes Pol II from the DNA template. Here we present three cryo-electron microscopy structures of the complete Integrator-PP2A complex in different functional states. The structure of the pre-termination complex reveals a previously unresolved, scorpion-tail-shaped INTS10-INTS13-INTS14-INTS15 module that may use its 'sting' to open the DSIF DNA clamp and facilitate termination. The structure of the post-termination complex shows that the previously unresolved subunit INTS3 and associated sensor of single-stranded DNA complex (SOSS) factors prevent Pol II rebinding to Integrator after termination. The structure of the free Integrator-PP2A complex in an inactive closed conformation reveals that INTS6 blocks the PP2A phosphatase active site. These results lead to a model for how Integrator terminates Pol II transcription in three steps that involve major rearrangements.
History
DepositionDec 5, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
B: SOSS complex subunit B1
C: SOSS complex subunit C
Y: DNA-directed RNA polymerase subunit
a: Integrator complex subunit 1
b: Integrator complex subunit 2
c: Integrator complex subunit 3
d: Integrator complex subunit 4
e: Integrator complex subunit 5
f: Integrator complex subunit 6
g: Integrator complex subunit 7
h: Integrator complex subunit 8
i: Integrator complex subunit 9
j: Integrator complex subunit 10
k: Integrator complex subunit 11
n: Integrator complex subunit 14
o: Integrator complex subunit 15
p: Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
q: Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
r: DSS1
m: Integrator complex subunit 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,588,87525
Polymers1,588,63421
Non-polymers2414
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein/peptide , 3 types, 3 molecules 1Yr

#1: Protein/peptide UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK


Mass: 783.958 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#4: Protein/peptide DNA-directed RNA polymerase subunit


Mass: 1356.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LJR4, DNA-directed RNA polymerase
#20: Protein/peptide DSS1


Mass: 3383.542 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper)

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SOSS complex subunit ... , 2 types, 2 molecules BC

#2: Protein SOSS complex subunit B1


Mass: 22566.053 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NABP2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BQ15
#3: Protein SOSS complex subunit C


Mass: 11642.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INIP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NRY2

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Integrator complex subunit ... , 14 types, 14 molecules abcdefghijknom

#5: Protein Integrator complex subunit 1


Mass: 244776.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8N201
#6: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H0H0
#7: Protein Integrator complex subunit 3


Mass: 118155.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q68E01
#8: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q96HW7
#9: Protein Integrator complex subunit 5


Mass: 108316.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS5 / Production host: Trichoplusia (butterflies/moths) / References: UniProt: Q6P9B9
#10: Protein Integrator complex subunit 6


Mass: 100728.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS6 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9UL03
#11: Protein Integrator complex subunit 7


Mass: 107153.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS7 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVH2
#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: Trichoplusia ni (cabbage looper) / References: UniProt: Q75QN2
#13: 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: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NV88
#14: Protein Integrator complex subunit 10 / Int10


Mass: 82339.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS10, C8orf35 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVR2
#15: Protein Integrator complex subunit 11


Mass: 67970.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS11 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5TA45
#16: Protein Integrator complex subunit 14 / von Willebrand factor A domain-containing protein 9


Mass: 57526.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS14, C15orf44, VWA9 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96SY0
#17: Protein Integrator complex subunit 15


Mass: 50303.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS15 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96N11
#21: Protein Integrator complex subunit 13 / Cell cycle regulator Mat89Bb homolog / Germ cell tumor 1 / Protein asunder homolog / Sarcoma antigen NY-SAR-95


Mass: 80345.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: INTS13, ASUN, C12orf11, GCT1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9NVM9

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

#18: Protein Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform


Mass: 65579.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2R1A / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P30153
#19: Protein Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform


Mass: 35836.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPP2CA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P67775

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Non-polymers , 2 types, 4 molecules

#22: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#23: 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

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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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Post-termination complexCOMPLEXIntegrator-PP2A, RNA Polymerase II C-terminal domain peptides, NABP2, INIP#1-#210MULTIPLE SOURCES
2Integrator-PP2A complex and NABP2 and INIPCOMPLEX#1, #41RECOMBINANT
3RNA Polymerase II C-terminal domain peptidesCOMPLEX#2-#3, #5-#19, #211NATURAL
4DSS1COMPLEX#201NATURAL
Molecular weightValue: 1.2 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Sus scrofa (pig)9823
44Trichoplusia ni (cabbage looper)7111
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.4
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 39.93 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 236382 / Symmetry type: POINT
Atomic model building
ID
1
2
Atomic model building
ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
114OWW1PDBexperimental model
228RBX2PDBexperimental model

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