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- PDB-8rbx: Structure of Integrator-PP2A bound to a paused RNA polymerase II-... -

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Basic information

Entry
Database: PDB / ID: 8rbx
TitleStructure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex
Components
  • (DNA-directed RNA polymerase ...) x 7
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 3
  • (Integrator complex subunit ...) x 13
  • (Negative elongation factor ...) x 2
  • (RNA polymerase II subunit ...) x 2
  • (Serine/threonine-protein phosphatase 2A ...) x 2
  • (UNK-UNK-UNK-UNK-UNK-UNK-UNK- ...) x 2
  • DSS1
  • Histone H2A type 1
  • Histone H2B type 1-J
  • Histone H3.3C
  • Histone H4
  • NELF-B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B
  • RNA
  • Template DNA
  • Transcription elongation factor SPT5
  • non-template DNA
KeywordsTRANSCRIPTION / Integrator complex / Pre-termination complex
Function / homology
Function and homology information


U2 snRNA 3'-end processing / regulation of fertilization / NELF complex / positive regulation of protein modification process / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation ...U2 snRNA 3'-end processing / regulation of fertilization / NELF complex / positive regulation of protein modification process / meiotic spindle elongation / Integration of energy metabolism / PP2A-mediated dephosphorylation of key metabolic factors / regulation of microtubule binding / NTRK3 as a dependence receptor / negative regulation of DNA-templated transcription, elongation / snRNA 3'-end processing / MASTL Facilitates Mitotic Progression / regulation of meiotic cell cycle process involved in oocyte maturation / mitotic sister chromatid separation / protein serine/threonine phosphatase complex / protein phosphatase type 2A complex / meiotic sister chromatid cohesion, centromeric / snRNA processing / peptidyl-serine dephosphorylation / peptidyl-threonine dephosphorylation / flagellated sperm motility / FAR/SIN/STRIPAK complex / DSIF complex / protein localization to nuclear envelope / Regulation of glycolysis by fructose 2,6-bisphosphate metabolism / positive regulation of microtubule binding / Inhibition of replication initiation of damaged DNA by RB1/E2F1 / female meiotic nuclear division / protein phosphatase regulator activity / protein antigen binding / GABA receptor binding / integrator complex / regulation of transcription elongation by RNA polymerase II / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / 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 / 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 / Initiation of Nuclear Envelope (NE) Reformation / negative regulation of stem cell differentiation / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / ERKs are inactivated / 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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / positive regulation of DNA-templated transcription, elongation / regulation of growth / Abortive elongation of HIV-1 transcript in the absence of Tat / Disassembly of the destruction complex and recruitment of AXIN to the membrane / inner cell mass cell proliferation / negative regulation of epithelial to mesenchymal transition / centrosome localization / negative regulation of glycolytic process through fructose-6-phosphate / transcription elongation-coupled chromatin remodeling / positive regulation of NLRP3 inflammasome complex assembly / Platelet sensitization by LDL / CTLA4 inhibitory signaling / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / protein serine/threonine phosphatase activity / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / myosin phosphatase activity / mRNA Capping / protein-serine/threonine phosphatase / regulation of cell differentiation / RNA polymerase III activity / T cell homeostasis / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / ERK/MAPK targets / mesoderm development / negative regulation of transcription elongation by RNA polymerase II / regulation of G1/S transition of mitotic cell cycle / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / positive regulation of macroautophagy / phosphoprotein phosphatase activity
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 / : / : / : / Integrator complex subunit 1, RP2B-binding domain / Integrator complex subunit 2 ...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 / : / INTS6/SAGE1/DDX26B/CT45, C-terminal / INTS6/SAGE1/DDX26B/CT45 C-terminus / Integrator complex subunit 10 / Integrator complex subunit 15 / Integrator complex subunit 5, C-terminal / Integrator complex subunit 5, N-terminal / Integrator complex subunit 8 / Integrator complex subunit 14 / Integrator complex subunit 5 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, C-terminal / Integrator complex subunit 5 N-terminus / Integrator complex subunit 5 C-terminus / Integrator complex subunit 15 / Integrator complex subunit 14, beta-barrel domain / Integrator complex subunit 14, alpha-helical domain / Integrator subunit 10 / Cell cycle regulator Mat89Bb / Cell cycle and development regulator Mat89Bb / Cofactor of BRCA1 / Cofactor of BRCA1 (COBRA1) / : / TH1 protein / TH1 protein / Hepatitis delta antigen (HDAg) domain / Hepatitis delta antigen (HDAg) domain profile. / 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 / Spt5, KOW domain repeat 6 / : / Beta-Casp domain / Beta-Casp domain / Beta-Casp domain / Zn-dependent metallo-hydrolase, RNA specificity domain / Zn-dependent metallo-hydrolase RNA specificity domain / Transcription elongation factor Spt5, eukaryote / Spt5 transcription elongation factor, N-terminal / Spt5, KOW domain repeat 2 / Spt5, KOW domain repeat 3 / Spt5, KOW domain repeat 5 / Spt5 transcription elongation factor, acidic N-terminal / NGN domain, eukaryotic / Spt5, KOW domain repeat 1 / Spt5, KOW domain repeat 4 / HEAT repeat / Spt5 C-terminal domain / Spt5 C-terminal nonapeptide repeat binding Spt4 / HEAT repeat / NGN domain / Transcription elongation factor SPT5 / Early transcription elongation factor of RNA pol II, NGN section / 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 / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / Calcineurin-like phosphoesterase domain, ApaH type / Calcineurin-like phosphoesterase / DNA-directed RNA polymerase II subunit Rpb4-like / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / Metallo-dependent phosphatase-like / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase subunit ...: / DNA / DNA (> 10) / DNA (> 100) / RNA / RNA (> 10) / RNA polymerase II subunit D / DNA-directed RNA polymerase subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase subunit / RNA polymerase II subunit K / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase II subunit RPB11-a / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase subunit beta / DNA-directed RNA polymerase II subunit E / Transcription elongation factor SPT5 / Histone H2A type 1 / Histone H2B type 1-J / Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform / DNA-directed RNA polymerase II subunit RPB9 / Histone H4 / Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform / Integrator complex subunit 11 / Histone H3.3C / Integrator complex subunit 5 / Integrator complex subunit 8 / Negative elongation factor C/D / Integrator complex subunit 1 / Negative elongation factor B / Integrator complex subunit 4 / Integrator complex subunit 15 / Integrator complex subunit 14 / Integrator complex subunit 2 / Negative elongation factor A / 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)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 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
A: DNA-directed RNA polymerase subunit
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: RNA polymerase II subunit D
E: DNA-directed RNA polymerase II subunit E
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
G: DNA-directed RNA polymerase II subunit RPB7
H: DNA-directed RNA polymerases I, II, and III subunit RPABC3
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11-a
L: RNA polymerase II subunit K
M: Histone H3.3C
N: non-template DNA
O: Histone H4
P: RNA
Q: Histone H2A type 1
R: Histone H2B type 1-J
S: Histone H3.3C
T: Template DNA
U: Histone H4
V: Histone H2A type 1
W: Histone H2B type 1-J
Y: DNA-directed RNA polymerase subunit
Z: Transcription elongation factor SPT5
a: Integrator complex subunit 1
b: Integrator complex subunit 2
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
m: Integrator complex subunit 13
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
u: Negative elongation factor A
v: NELF-B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B
w: Negative elongation factor C/D
x: UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,703,21159
Polymers2,702,42346
Non-polymers78813
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, Gradient centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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UNK-UNK-UNK-UNK-UNK-UNK-UNK- ... , 2 types, 2 molecules 1x

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


Mass: 698.854 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
#41: Protein/peptide UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK


Mass: 1890.321 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia ni (cabbage looper)

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DNA-directed RNA polymerase ... , 7 types, 8 molecules AYBCEGIK

#2: Protein DNA-directed RNA polymerase subunit


Mass: 217450.078 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig)
References: UniProt: A0A7M4DUC2, DNA-directed RNA polymerase
#3: Protein DNA-directed RNA polymerase subunit beta


Mass: 134041.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LGP4, DNA-directed RNA polymerase
#4: Protein DNA-directed RNA polymerase II subunit RPB3


Mass: 31439.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCH3
#6: Protein DNA-directed RNA polymerase II subunit E / RPB5 homolog


Mass: 24644.318 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LSI7
#8: Protein DNA-directed RNA polymerase II subunit RPB7


Mass: 19314.283 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VKG7
#10: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 ...RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I / RNA polymerase II 14.5 kDa subunit / RPB14.5


Mass: 14541.221 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P60899
#12: Protein DNA-directed RNA polymerase II subunit RPB11-a


Mass: 13310.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: F1RKE4

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RNA polymerase II subunit ... , 2 types, 2 molecules DL

#5: Protein RNA polymerase II subunit D


Mass: 16331.255 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A287ADR4
#13: Protein RNA polymerase II subunit K


Mass: 7018.244 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D0JYF1

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DNA-directed RNA polymerases I, II, and III subunit ... , 3 types, 3 molecules FHJ

#7: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2


Mass: 14477.001 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A8D1KNW4
#9: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3


Mass: 17162.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: I3LCB2
#11: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5


Mass: 7655.123 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: A0A4X1VYD0

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Protein , 6 types, 10 molecules MSOUQVRWZv

#14: Protein Histone H3.3C


Mass: 15350.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3-5 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6NXT2
#16: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, ...Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#18: Protein Histone H2A type 1


Mass: 14093.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MSGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKTESHHKAKGK
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02262
#19: Protein Histone H2B type 1-J


Mass: 13981.267 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11 / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#21: Protein Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing ...hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 121145.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Escherichia coli (E. coli) / References: UniProt: O00267
#39: Protein NELF-B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B / NELF-B / Cofactor of BRCA1


Mass: 68587.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELFB, COBRA1, KIAA1182 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8WX92

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DNA chain , 2 types, 2 molecules NT

#15: DNA chain non-template DNA


Mass: 45938.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#20: DNA chain Template DNA


Mass: 56757.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Integrator complex subunit ... , 13 types, 13 molecules abdefghijkmno

#22: 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
#23: 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
#24: 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
#25: 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 ni (cabbage looper) / References: UniProt: Q6P9B9
#26: 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
#27: 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
#28: 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
#29: 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
#30: 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
#31: Protein Integrator complex subunit 11


Mass: 67956.750 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
#32: 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
#33: 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
#34: 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

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

#35: 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
#36: 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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Negative elongation factor ... , 2 types, 2 molecules uw

#38: Protein Negative elongation factor A / NELF-A / Wolf-Hirschhorn syndrome candidate 2 protein


Mass: 57343.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELFA, WHSC2, P/OKcl.15 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9H3P2
#40: Protein Negative elongation factor C/D / NELF-C/D / TH1-like protein


Mass: 65748.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NELFCD, NELFD, TH1, TH1L, HSPC130 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8IXH7

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RNA chain / Protein/peptide , 2 types, 2 molecules Pr

#17: RNA chain RNA


Mass: 5549.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#37: Protein/peptide DSS1


Mass: 3558.796 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trichoplusia ni (cabbage looper)

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Non-polymers , 3 types, 13 molecules

#42: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn
#43: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#44: 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
1Pre-termination complexCOMPLEXIntegrator-PP2A, RNA Polymerase II, NELF, DSIF, nucleosome#1-#410MULTIPLE SOURCES
2Integrator-PP2A complex and NELFCOMPLEX#22-#36, #38-#411RECOMBINANT
3NucleosomeCOMPLEX#14, #16, #18-#19, #211RECOMBINANT
5RNA and DNACOMPLEX#15, #17, #201RECOMBINANT
4DNA-directed RNA Polymerase IICOMPLEX#1-#131NATURAL
6DSIFCOMPLEX#371NATURAL
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Homo sapiens (human)9606
55Sus scrofa (pig)9823
66Trichoplusia ni (cabbage looper)7111
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Trichoplusia ni (cabbage looper)7111
33Escherichia coli (E. coli)562
44synthetic construct (others)32630
Buffer solutionpH: 7.4
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Qu
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: 40.44 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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 80717 / Symmetry type: POINT
Atomic model building
ID
1
2
3
4
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17PKS

7pks

17PKS1PDBexperimental model
27OHC

7ohc

27OHC2PDBexperimental model
36SN1

6sn1

36SN13PDBexperimental model
44AlphaFoldin silico model

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