8JJ6 | pdb_00008jj6

Structure of the NELF-BCE complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free: 
    0.262 (Depositor), 0.257 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.209 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structural basis of the human negative elongation factor NELF-B/C/E ternary complex.

Cao, Y.Qin, Y.Zhang, W.Tian, W.Ren, Y.Ren, J.Wang, J.Wang, M.Jiang, J.Wang, Z.

(2023) Biochem Biophys Res Commun 677: 155-161

  • DOI: https://doi.org/10.1016/j.bbrc.2023.08.019
  • Primary Citation Related Structures: 
    8JJ6

  • PubMed Abstract: 

    Negative elongation factor (NELF) is a four-subunit transcription elongation factor that mainly functions in maintaining the paused state of RNA polymerase II in eukaryotes. Upon binding to Pol II, NELF works synergistically with DRB sensitivity-inducing factor (DSIF) and inhibits transcription elongation of Pol II, which subsequently retains a stably paused state 20-60 base pairs downstream of the promoter. The promoter-proximal pausing of Pol II caused by NELF is a general mechanism of transcriptional regulation for most signal-responsive genes. To date, structural studies have significantly advanced our understanding of the molecular mechanisms of NELF. However, a high quality structural model clarifying the interaction details of this complex is still lacking. In this study, we solved the high resolution crystal structure of the NELF-B/C/E ternary complex. We observed detailed interactions between subunits and identified residues important for the association between NELF-B and NELF-E. Our work presents a precise model of the NELF complex, which will facilitate our understanding of its in vivo function.


  • Organizational Affiliation
    • Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing, 100875, China.

Macromolecule Content 

  • Total Structure Weight: 172.89 kDa 
  • Atom Count: 11,833 
  • Modeled Residue Count: 1,462 
  • Deposited Residue Count: 1,516 
  • Unique protein chains: 3

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Negative elongation factor BA,
C [auth B]
560Homo sapiensMutation(s): 0 
Gene Names: NELFB
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Negative elongation factor complex member C/DB [auth D],
D [auth C]
147Homo sapiensMutation(s): 0 
Gene Names: NELFCD
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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
NELF-E
E, F
51Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P18615 (Homo sapiens)
Explore P18615 
Go to UniProtKB:  P18615
PHAROS:  P18615
GTEx:  ENSG00000204356 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18615
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.72 Å
  • R-Value Free:  0.262 (Depositor), 0.257 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.209 (Depositor) 
Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 156.614α = 90
b = 166.709β = 90
c = 75.025γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870725

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-30
    Type: Initial release
  • Version 1.1: 2024-09-11
    Changes: Database references