5L3X

Crystal structure of negative elongation factor subcomplex NELF-AC


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Architecture and RNA binding of the human negative elongation factor.

Vos, S.M.Pollmann, D.Caizzi, L.Hofmann, K.B.Rombaut, P.Zimniak, T.Herzog, F.Cramer, P.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.14981
  • Primary Citation of Related Structures:  
    5L3X

  • PubMed Abstract: 

    Transcription regulation in metazoans often involves promoter-proximal pausing of RNA polymerase (Pol) II, which requires the 4-subunit negative elongation factor (NELF). Here we discern the functional architecture of human NELF through X-ray crystallography, protein crosslinking, biochemical assays, and RNA crosslinking in cells. We identify a NELF core subcomplex formed by conserved regions in subunits NELF-A and NELF-C, and resolve its crystal structure. The NELF-AC subcomplex binds single-stranded nucleic acids in vitro, and NELF-C associates with RNA in vivo. A positively charged face of NELF-AC is involved in RNA binding, whereas the opposite face of the NELF-AC subcomplex binds NELF-B. NELF-B is predicted to form a HEAT repeat fold, also binds RNA in vivo, and anchors the subunit NELF-E, which is confirmed to bind RNA in vivo. These results reveal the three-dimensional architecture and three RNA-binding faces of NELF.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor A177Homo 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
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Negative elongation factor C/D405Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.238 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.07α = 90
b = 185.07β = 90
c = 185.07γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
SHELXDEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB 860
European Research CouncilGermanyTRANSIT
Volkswagen FoundationGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-22
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Data collection
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence, Refinement description
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references