8RBX

Structure of Integrator-PP2A bound to a paused RNA polymerase II-DSIF-NELF-nucleosome complex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 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. 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 8RBZ 8RC4


Literature

Structural basis of Integrator-dependent RNA polymerase II termination.

Fianu, I., Ochmann, M., Walshe, J.L., Dybkov, O., Cruz, J.N., Urlaub, H., Cramer, P.

(2024) Nature 

  • DOI: https://doi.org/10.1038/s41586-024-07269-4
  • Primary Citation of Related Structures:  
    8RBX, 8RBZ, 8RC4

  • PubMed 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 consisting of Pol II, the DRB sensitivity-inducing factor (DSIF) and the negative elongation factor (NELF) and how it cleaves the nascent RNA transcript 1 , 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 2 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.

    • Organizational Affiliation: 

    Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. isaac.fianu@mpinat.mpg.de.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNKA [auth 1]8Sus scrofaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitB [auth A],
Y		1,970Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A7M4DUC2 (Sus scrofa)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC [auth B]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3D [auth C]275Sus scrofaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit DE [auth D]142Sus scrofaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EF [auth E]210Sus scrofaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2G [auth F]127Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7H [auth G]172Sus scrofaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3I [auth H]150Sus scrofaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9J [auth I]125Sus scrofaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5K [auth J]67Sus scrofaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11-aL [auth K]117Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit KM [auth L]58Sus scrofaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H3.3CN [auth M],
T [auth S]		135Homo sapiensMutation(s): 0 
Gene Names: H3-5
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GTEx:  ENSG00000188375 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4P [auth O],
V [auth U]		103Homo sapiensMutation(s): 0 
Gene Names: 
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GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2A type 1R [auth Q],
W [auth V]		130Homo sapiensMutation(s): 1 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H2B type 1-JS [auth R],
X [auth W]		126Homo sapiensMutation(s): 0 
Gene Names: H2BC11
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GTEx:  ENSG00000124635 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT51,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5H, SPT5, SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 1AA [auth a]2,192Homo sapiensMutation(s): 0 
Gene Names: INTS1
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GTEx:  ENSG00000164880 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 2BA [auth b]1,204Homo sapiensMutation(s): 0 
Gene Names: INTS2, KIAA1287
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GTEx:  ENSG00000108506 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 4CA [auth d]963Homo sapiensMutation(s): 0 
Gene Names: INTS4, MSTP093
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GTEx:  ENSG00000149262 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 5DA [auth e]1,021Homo sapiensMutation(s): 0 
Gene Names: INTS5
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GTEx:  ENSG00000185085 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 6EA [auth f]889Homo sapiensMutation(s): 0 
Gene Names: INTS6
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GTEx:  ENSG00000102786 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 7FA [auth g]964Homo sapiensMutation(s): 0 
Gene Names: INTS7
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GTEx:  ENSG00000143493 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 8GA [auth h]995Homo sapiensMutation(s): 0 
Gene Names: INTS8, C8orf52
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GTEx:  ENSG00000164941 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 9HA [auth i]658Homo sapiensMutation(s): 0 
Gene Names: INTS9, RC74
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GTEx:  ENSG00000104299 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 10IA [auth j]710Homo sapiensMutation(s): 0 
Gene Names: INTS10, C8orf35
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GTEx:  ENSG00000104613 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 11JA [auth k]602Homo sapiensMutation(s): 1 
Gene Names: INTS11
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GTEx:  ENSG00000127054 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 13KA [auth m]706Homo sapiensMutation(s): 0 
Gene Names: INTS13, ASUN, C12orf11, GCT1
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GTEx:  ENSG00000064102 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 14LA [auth n]518Homo sapiensMutation(s): 0 
Gene Names: INTS14, C15orf44, VWA9
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GTEx:  ENSG00000138614 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 15MA [auth o]451Homo sapiensMutation(s): 0 
Gene Names: INTS15
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GTEx:  ENSG00000146576 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoformNA [auth p]591Homo sapiensMutation(s): 0 
Gene Names: PPP2R1A
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GTEx:  ENSG00000105568 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoformOA [auth q]311Homo sapiensMutation(s): 1 
Gene Names: PPP2CA
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GTEx:  ENSG00000113575 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
DSS1PA [auth r]28Trichoplusia niMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor AQA [auth u]528Homo sapiensMutation(s): 0 
Gene Names: NELFA, WHSC2, P/OKcl.15
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GTEx:  ENSG00000185049 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
NELF-B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor B,Negative elongation factor BRA [auth v]613Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000188986 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor C/DSA [auth w]583Homo sapiensMutation(s): 0 
Gene Names: NELFCD, NELFD, TH1, TH1L, HSPC130
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GTEx:  ENSG00000101158 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNK-UNKTA [auth x]22Homo sapiensMutation(s): 0 
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Entity ID: 15
MoleculeChains LengthOrganismImage
non-template DNAO [auth N]148synthetic construct
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Entity ID: 17
MoleculeChains LengthOrganismImage
RNAQ [auth P]17synthetic construct
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Entity ID: 20
MoleculeChains LengthOrganismImage
Template DNAU [auth T]185synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
AB [auth J]
BB [auth L]
EB [auth k]
FB [auth k]
UA [auth A]
AB [auth J],
BB [auth L],
EB [auth k],
FB [auth k],
UA [auth A],
VA [auth A],
WA [auth B],
XA [auth C],
YA [auth I],
ZA [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN
Query on MN
Download Ideal Coordinates CCD File 
DB [auth f],
GB [auth q]		MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
CB [auth P]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB860
German Research Foundation (DFG)GermanySFB1565
European Research Council (ERC)European UnionEXC 2067/1-390729940

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release
  • Version 1.1: 2024-04-10
    Changes: Database references