8UIS

Structure of transcription complex Pol II-DSIF-NELF-TFIIS


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 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


Literature

Distinct negative elongation factor conformations regulate RNA polymerase II promoter-proximal pausing.

Su, B.G.Vos, S.M.

(2024) Mol Cell 84: 1243

  • DOI: https://doi.org/10.1016/j.molcel.2024.01.023
  • Primary Citation of Related Structures:  
    8UHA, 8UHD, 8UHG, 8UI0, 8UIS

  • PubMed Abstract: 

    Metazoan gene expression regulation involves pausing of RNA polymerase (Pol II) in the promoter-proximal region of genes and is stabilized by DSIF and NELF. Upon depletion of elongation factors, NELF appears to accompany elongating Pol II past pause sites; however, prior work indicates that NELF prevents Pol II elongation. Here, we report cryoelectron microscopy structures of Pol II-DSIF-NELF complexes with NELF in two distinct conformations corresponding to paused and poised states. The paused NELF state supports Pol II stalling, whereas the poised NELF state enables transcription elongation as it does not support a tilted RNA-DNA hybrid. Further, the poised NELF state can accommodate TFIIS binding to Pol II, allowing for Pol II reactivation at paused or backtracking sites. Finally, we observe that the NELF-A tentacle interacts with the RPB2 protrusion and is necessary for pausing. Our results define how NELF can support pausing, reactivation, and elongation by Pol II.


  • Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Building 68, 31 Ames St., Cambridge, MA 02139, USA.


Macromolecules

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor C/DD [auth W]590Homo sapiensMutation(s): 0 
Gene Names: NELFCDNELFDTH1TH1LHSPC130
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PHAROS:  Q8IXH7
GTEx:  ENSG00000101158 
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UniProt GroupQ8IXH7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5E [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunitF [auth A]1,970Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaG [auth B]1,174Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3H [auth C]271Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase Rpb4/RPC9 core domain-containing proteinI [auth D]142Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit EJ [auth E]210Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2K [auth F]127Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7L [auth G]172Sus scrofaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3M [auth H]150Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9N [auth I]125Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5O [auth J]67Sus scrofaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit JP [auth K]117Sus scrofaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit KQ [auth L]58Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor A protein 1R [auth S]301Homo sapiensMutation(s): 0 
Gene Names: TCEA1GTF2STFIIS
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GTEx:  ENSG00000187735 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor AS [auth U]528Homo sapiensMutation(s): 0 
Gene Names: NELFAWHSC2P/OKcl.15
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GTEx:  ENSG00000185049 
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Entity ID: 1
MoleculeChains LengthOrganismImage
Non-template DNAA [auth N]50synthetic construct
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Entity ID: 2
MoleculeChains LengthOrganismImage
RNAB [auth P]22synthetic construct
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Entity ID: 3
MoleculeChains LengthOrganismImage
Template DNAC [auth T]50synthetic construct
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth L]
T [auth A]
U [auth A]
W [auth B]
AA [auth J],
BA [auth L],
T [auth A],
U [auth A],
W [auth B],
X [auth C],
Y [auth I],
Z [auth I]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesDP2-GM146254

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-20
    Type: Initial release
  • Version 1.1: 2024-04-17
    Changes: Database references