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 

wwPDB Validation   3D Report Full Report


This is version 1.0 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore A0A7M4DUC2 
Go to UniProtKB:  A0A7M4DUC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7M4DUC2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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)
Explore A0A0B8RVL1 
Go to UniProtKB:  A0A0B8RVL1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B8RVL1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A481DF93 (Sus scrofa)
Explore A0A481DF93 
Go to UniProtKB:  A0A481DF93
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A481DF93
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit D142Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A287ADR4 (Sus scrofa)
Explore A0A287ADR4 
Go to UniProtKB:  A0A287ADR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A287ADR4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for I3LSI7 (Sus scrofa)
Explore I3LSI7 
Go to UniProtKB:  I3LSI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LSI7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit F127Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa)
Explore A0A4X1VEK9 
Go to UniProtKB:  A0A4X1VEK9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1VEK9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Sus scrofa domesticusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for I3LCB2 (Sus scrofa)
Explore I3LCB2 
Go to UniProtKB:  I3LCB2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LCB2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for P60899 (Sus scrofa)
Explore P60899 
Go to UniProtKB:  P60899
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60899
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A7K6NXI9 (Pedionomus torquatus)
Explore A0A7K6NXI9 
Go to UniProtKB:  A0A7K6NXI9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7K6NXI9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing protein117Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for F1RKE4 (Sus scrofa)
Explore F1RKE4 
Go to UniProtKB:  F1RKE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF1RKE4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit K58Sus scrofa domesticusMutation(s): 0 
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa)
Explore A0A4X1TRS6 
Go to UniProtKB:  A0A4X1TRS6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4X1TRS6
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RPBI C-terminal domain peptide13Sus scrofa domesticusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LJR4 (Sus scrofa)
Explore I3LJR4 
Go to UniProtKB:  I3LJR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3LJR4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor AQ [auth U]528Homo sapiensMutation(s): 0 
Gene Names: NELFAWHSC2P/OKcl.15
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H3P2 (Homo sapiens)
Explore Q9H3P2 
Go to UniProtKB:  Q9H3P2
PHAROS:  Q9H3P2
GTEx:  ENSG00000185049 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H3P2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor BR [auth V]614Homo sapiensMutation(s): 0 
Gene Names: NELFBCOBRA1KIAA1182
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WX92 (Homo sapiens)
Explore Q8WX92 
Go to UniProtKB:  Q8WX92
PHAROS:  Q8WX92
GTEx:  ENSG00000188986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WX92
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor C/DS [auth W]616Homo sapiensMutation(s): 0 
Gene Names: NELFCDNELFDTH1TH1LHSPC130
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXH7 (Homo sapiens)
Explore Q8IXH7 
Go to UniProtKB:  Q8IXH7
PHAROS:  Q8IXH7
GTEx:  ENSG00000101158 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IXH7
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor ET [auth X]22Homo sapiensMutation(s): 0 
Gene Names: NELFERDRDBP
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
Find proteins for O00267 (Homo sapiens)
Explore O00267 
Go to UniProtKB:  O00267
PHAROS:  O00267
GTEx:  ENSG00000196235 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00267
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 1V [auth a]2,190Homo sapiensMutation(s): 0 
Gene Names: INTS1KIAA1440UNQ1821/PRO3434
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N201 (Homo sapiens)
Explore Q8N201 
Go to UniProtKB:  Q8N201
PHAROS:  Q8N201
GTEx:  ENSG00000164880 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N201
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 2W [auth b]1,204Homo sapiensMutation(s): 0 
Gene Names: INTS2KIAA1287
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H0H0 (Homo sapiens)
Explore Q9H0H0 
Go to UniProtKB:  Q9H0H0
PHAROS:  Q9H0H0
GTEx:  ENSG00000108506 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H0H0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 4X [auth d]963Homo sapiensMutation(s): 0 
Gene Names: INTS4MSTP093
UniProt & NIH Common Fund Data Resources
Find proteins for Q96HW7 (Homo sapiens)
Explore Q96HW7 
Go to UniProtKB:  Q96HW7
PHAROS:  Q96HW7
GTEx:  ENSG00000149262 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96HW7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 5Y [auth e]1,019Homo sapiensMutation(s): 0 
Gene Names: INTS5KIAA1698
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P9B9 (Homo sapiens)
Explore Q6P9B9 
Go to UniProtKB:  Q6P9B9
PHAROS:  Q6P9B9
GTEx:  ENSG00000185085 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6P9B9
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 6Z [auth f]887Homo sapiensMutation(s): 0 
Gene Names: INTS6DBI1DDX26DDX26A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL03 (Homo sapiens)
Explore Q9UL03 
Go to UniProtKB:  Q9UL03
PHAROS:  Q9UL03
GTEx:  ENSG00000102786 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UL03
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 7AA [auth g]962Homo sapiensMutation(s): 0 
Gene Names: INTS7C1orf73
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NVH2 (Homo sapiens)
Explore Q9NVH2 
Go to UniProtKB:  Q9NVH2
PHAROS:  Q9NVH2
GTEx:  ENSG00000143493 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NVH2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 8BA [auth h]995Homo sapiensMutation(s): 0 
Gene Names: INTS8C8orf52
UniProt & NIH Common Fund Data Resources
Find proteins for Q75QN2 (Homo sapiens)
Explore Q75QN2 
Go to UniProtKB:  Q75QN2
PHAROS:  Q75QN2
GTEx:  ENSG00000164941 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ75QN2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 9CA [auth i]658Homo sapiensMutation(s): 0 
Gene Names: INTS9RC74
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NV88 (Homo sapiens)
Explore Q9NV88 
Go to UniProtKB:  Q9NV88
PHAROS:  Q9NV88
GTEx:  ENSG00000104299 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NV88
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Integrator complex subunit 11DA [auth k]600Homo sapiensMutation(s): 0 
Gene Names: INTS11CPSF3LRC68
EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q5TA45 (Homo sapiens)
Explore Q5TA45 
Go to UniProtKB:  Q5TA45
PHAROS:  Q5TA45
GTEx:  ENSG00000127054 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5TA45
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
UniProt & NIH Common Fund Data Resources
Find proteins for P30153 (Homo sapiens)
Explore P30153 
Go to UniProtKB:  P30153
PHAROS:  P30153
GTEx:  ENSG00000105568 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30153
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
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
UniProt & NIH Common Fund Data Resources
Find proteins for P67775 (Homo sapiens)
Explore P67775 
Go to UniProtKB:  P67775
PHAROS:  P67775
GTEx:  ENSG00000113575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67775
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
UnknownGA [auth u]27Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains LengthOrganismImage
Non-template DNA48Human immunodeficiency virus 1
Sequence Annotations
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 15
MoleculeChains LengthOrganismImage
TAR RNAO [auth P]17Human immunodeficiency virus 1
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains LengthOrganismImage
DNA TemplateP [auth T]48Human immunodeficiency virus 1
Sequence Annotations
Expand
  • Reference Sequence
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

View Full Validation Report



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