7PKS

Structural basis of Integrator-mediated transcription regulation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of Integrator-mediated transcription regulation.

Fianu, I.Chen, Y.Dienemann, C.Dybkov, O.Linden, A.Urlaub, H.Cramer, P.

(2021) Science 374: 883-887

  • DOI: https://doi.org/10.1126/science.abk0154
  • Primary Citation of Related Structures:  
    7PKS

  • PubMed Abstract: 

    Integrator and protein phosphatase 2A (PP2A) form a complex that dephosphorylates paused RNA polymerase II (Pol II), cleaves the nascent RNA, and terminates transcription. We report the structure of the pretermination complex containing the human Integrator-PP2A complex bound to paused Pol II. Integrator binds Pol II and the pausing factors DSIF and NELF to exclude binding of the elongation factors SPT6 and PAF1 complex. Integrator also binds the C-terminal domain of Pol II and positions PP2A to counteract Pol II phosphorylation and elongation. The Integrator endonuclease docks to the RNA exit site and opens to cleave nascent RNA about 20 nucleotides from the Pol II active site. Integrator does not bind the DNA clamps formed by Pol II and DSIF, enabling release of DNA and transcription termination.


  • Organizational Affiliation

    Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit1,970Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A7M4DUC2 (Sus scrofa)
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UniProt GroupA0A7M4DUC2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,174Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for A0A0B8RVL1 (Sus scrofa domesticus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit D142Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit F127Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Sus scrofa domesticusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofa domesticusMutation(s): 0 
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Find proteins for A0A7K6NXI9 (Pedionomus torquatus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing protein117Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for F1RKE4 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit K58Sus scrofa domesticusMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RPBI C-terminal domain peptide13Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor AQ [auth U]528Homo sapiensMutation(s): 0 
Gene Names: NELFAWHSC2P/OKcl.15
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GTEx:  ENSG00000185049 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor BR [auth V]614Homo sapiensMutation(s): 0 
Gene Names: NELFBCOBRA1KIAA1182
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GTEx:  ENSG00000188986 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor C/DS [auth W]616Homo sapiensMutation(s): 0 
Gene Names: NELFCDNELFDTH1TH1LHSPC130
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GTEx:  ENSG00000101158 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor ET [auth X]22Homo sapiensMutation(s): 0 
Gene Names: NELFERDRDBP
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5U [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
UniProt & NIH Common Fund Data Resources
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PHAROS:  O00267
GTEx:  ENSG00000196235 
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UniProt GroupO00267
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 1V [auth a]2,190Homo sapiensMutation(s): 0 
Gene Names: INTS1KIAA1440UNQ1821/PRO3434
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GTEx:  ENSG00000164880 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 2W [auth b]1,204Homo sapiensMutation(s): 0 
Gene Names: INTS2KIAA1287
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PHAROS:  Q9H0H0
GTEx:  ENSG00000108506 
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UniProt GroupQ9H0H0
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 4X [auth d]963Homo sapiensMutation(s): 0 
Gene Names: INTS4MSTP093
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GTEx:  ENSG00000149262 
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UniProt GroupQ96HW7
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 5Y [auth e]1,019Homo sapiensMutation(s): 0 
Gene Names: INTS5KIAA1698
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GTEx:  ENSG00000185085 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 6Z [auth f]887Homo sapiensMutation(s): 0 
Gene Names: INTS6DBI1DDX26DDX26A
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GTEx:  ENSG00000102786 
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UniProt GroupQ9UL03
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 7AA [auth g]962Homo sapiensMutation(s): 0 
Gene Names: INTS7C1orf73
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Find proteins for Q9NVH2 (Homo sapiens)
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GTEx:  ENSG00000143493 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 8BA [auth h]995Homo sapiensMutation(s): 0 
Gene Names: INTS8C8orf52
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GTEx:  ENSG00000164941 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 9CA [auth i]658Homo sapiensMutation(s): 0 
Gene Names: INTS9RC74
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GTEx:  ENSG00000104299 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 11DA [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: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoformEA [auth p]589Homo sapiensMutation(s): 0 
Gene Names: PPP2R1A
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GTEx:  ENSG00000105568 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoformFA [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: 33
MoleculeChains Sequence LengthOrganismDetailsImage
UnknownGA [auth u]27Homo sapiensMutation(s): 0 
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Entity ID: 14
MoleculeChains LengthOrganismImage
Non-template DNA48Human immunodeficiency virus 1
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Entity ID: 15
MoleculeChains LengthOrganismImage
TAR RNAO [auth P]17Human immunodeficiency virus 1
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Entity ID: 16
MoleculeChains LengthOrganismImage
DNA TemplateP [auth T]48Human immunodeficiency virus 1
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN (Subject of Investigation/LOI)
Query on ZN

Download Ideal Coordinates CCD File 
IA [auth A]
JA [auth A]
KA [auth B]
LA [auth C]
MA [auth I]
IA [auth A],
JA [auth A],
KA [auth B],
LA [auth C],
MA [auth I],
NA [auth I],
OA [auth J],
PA [auth L],
QA [auth k],
RA [auth k]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)
Query on MN

Download Ideal Coordinates CCD File 
SA [auth q],
TA [auth q]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
HA [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.14
RECONSTRUCTIONRELION3.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)European UnionEXC 2067/1-390729940
European Research Council (ERC)European Union882357

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-08
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Refinement description, Structure summary