7OKY

Structure of active transcription elongation complex Pol II-DSIF-ELL2-EAF1(composite structure)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Allosteric transcription stimulation by RNA polymerase II super elongation complex.

Chen, Y.Vos, S.M.Dienemann, C.Ninov, M.Urlaub, H.Cramer, P.

(2021) Mol Cell 81: 3386-3399.e10

  • DOI: https://doi.org/10.1016/j.molcel.2021.06.019
  • Primary Citation of Related Structures:  
    7OKX, 7OKY, 7OL0

  • PubMed Abstract: 

    The super elongation complex (SEC) contains the positive transcription elongation factor b (P-TEFb) and the subcomplex ELL2-EAF1, which stimulates RNA polymerase II (RNA Pol II) elongation. Here, we report the cryoelectron microscopy (cryo-EM) structure of ELL2-EAF1 bound to a RNA Pol II elongation complex at 2.8 Å resolution. The ELL2-EAF1 dimerization module directly binds the RNA Pol II lobe domain, explaining how SEC delivers P-TEFb to RNA Pol II. The same site on the lobe also binds the initiation factor TFIIF, consistent with SEC binding only after the transition from transcription initiation to elongation. Structure-guided functional analysis shows that the stimulation of RNA elongation requires the dimerization module and the ELL2 linker that tethers the module to the RNA Pol II protrusion. Our results show that SEC stimulates elongation allosterically and indicate that this stimulation involves stabilization of a closed conformation of the RNA Pol II active center cleft.


  • Organizational Affiliation

    Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB11,970Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
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UniProt GroupA0A7M4DUC2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,251Sus scrofaMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa)
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UniProt GroupI3LGP4
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB3275Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupI3LCH3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit D184Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit E210Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupI3LSI7
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit F127Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB7172Sus scrofaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3150Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II subunit RPB9125Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC567Sus scrofaMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
RNA_pol_L_2 domain-containing protein117Sus scrofaMutation(s): 0 
UniProt
Find proteins for F1RKE4 (Sus scrofa)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II subunit K58Sus scrofaMutation(s): 0 
UniProt
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UniProt GroupA0A4X1TRS6
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase II elongation factor ELL2640Homo sapiensMutation(s): 0 
Gene Names: ELL2
UniProt & NIH Common Fund Data Resources
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PHAROS:  O00472
GTEx:  ENSG00000118985 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
ELL-associated factor 1268Homo sapiensMutation(s): 0 
Gene Names: EAF1
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GTEx:  ENSG00000144597 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT5R [auth Z]1,087Homo sapiensMutation(s): 0 
Gene Names: SUPT5HSPT5SPT5H
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GTEx:  ENSG00000196235 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription elongation factor SPT4S [auth Y]117Homo sapiensMutation(s): 0 
Gene Names: SUPT4H1SPT4HSUPT4H
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PHAROS:  P63272
GTEx:  ENSG00000213246 
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Entity ID: 14
MoleculeChains LengthOrganismImage
Non-template DNA48HIV whole-genome vector AA1305#18
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Entity ID: 16
MoleculeChains LengthOrganismImage
RNA47HIV whole-genome vector AA1305#18
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Entity ID: 17
MoleculeChains LengthOrganismImage
Template DNAQ [auth T]48HIV whole-genome vector AA1305#18
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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]
CA [auth Y]
U [auth A]
V [auth A]
AA [auth J],
BA [auth L],
CA [auth Y],
U [auth A],
V [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 
T [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.14 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanySFB860
German Research Foundation (DFG)GermanyEXC 2067/1-390729940
European Research Council (ERC)GermanyAdvanced Grant CHROMATRANS 693023
German Research Foundation (DFG)GermanySFB1286

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2021-07-21
    Changes: Database references, Source and taxonomy
  • Version 1.2: 2021-07-28
    Changes: Database references
  • Version 1.3: 2021-09-01
    Changes: Database references