6EIH | pdb_00006eih

The crystal structure of 14-3-3 epsilon in complex with the phosphorylated NELFE peptide

• PDB DOI: https://doi.org/10.2210/pdb6EIH/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens
• Expression System: unidentified plasmid, synthetic construct
• Mutation(s): No 


• Deposited: 2017-09-19 Released: 2018-02-14 
• Deposition Author(s): Akutsu, M., Wagner, S.A., Beli, P.
• Funding Organization(s): Emmy Noether Program, SFB, Marie Curie Career Integration Grant from the European Commission, LOEWE program Ubiquitin Networks

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.241 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.179 (Depositor) 

Literature

p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage.

Borisova, M.E., Voigt, A., Tollenaere, M.A.X., Sahu, S.K., Juretschke, T., Kreim, N., Mailand, N., Choudhary, C., Bekker-Jensen, S., Akutsu, M., Wagner, S.A., Beli, P.

(2018) Nat Commun 9: 1017-1017

• PubMed: 29523821 
• DOI: https://doi.org/10.1038/s41467-018-03417-3
• Primary Citation Related Structures: 
  6EIH


• PubMed Abstract: 
  

  Ultraviolet (UV) light radiation induces the formation of bulky photoproducts in the DNA that globally affect transcription and splicing. However, the signaling pathways and mechanisms that link UV-light-induced DNA damage to changes in RNA metabolism remain poorly understood. Here we employ quantitative phosphoproteomics and protein kinase inhibition to provide a systems view on protein phosphorylation patterns induced by UV light and uncover the dependencies of phosphorylation events on the canonical DNA damage signaling by ATM/ATR and the p38 MAP kinase pathway. We identify RNA-binding proteins as primary substrates and 14-3-3 as direct readers of p38-MK2-dependent phosphorylation induced by UV light. Mechanistically, we show that MK2 phosphorylates the RNA-binding subunit of the NELF complex NELFE on Serine 115. NELFE phosphorylation promotes the recruitment of 14-3-3 and rapid dissociation of the NELF complex from chromatin, which is accompanied by RNA polymerase II elongation.

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Organizational Affiliation: 
• Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany.
Cellular Stress Signaling Group, Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3C, 2200, Copenhagen, Denmark.
Ubiquitin Signaling Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
Proteomics and Cell Signaling Group, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
Institute of Biochemistry II, Goethe University Medical School, Theodor-Stern-Kai 7, 60590 Frankfurt and Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University, Max-von Laue-Strasse 15, 60438, Frankfurt, Germany.
Department of Medicine, Hematology/Oncology, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt, Germany.
German Cancer Consortium (DKTK), 69120, Heidelberg, Germany.
German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany.
Institute of Molecular Biology (IMB), Ackermannweg 4, 55128, Mainz, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 26.91 kDa 
• Atom Count: 1,859 
• Modeled Residue Count: 234 
• Deposited Residue Count: 234 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein epsilon	A	230	Homo sapiens	Mutation(s): 0  Gene Names: YWHAE
UniProt & NIH Common Fund Data Resources
Find proteins for P62258 (Homo sapiens) Explore P62258  Go to UniProtKB:  P62258
PHAROS:  P62258 GTEx:  ENSG00000108953

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SER-ILE-SEP-ARG	B [auth P]	4	Homo sapiens	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B [auth P]	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.241 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.179 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.29	α = 90
b = 81.186	β = 90
c = 81.05	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-02-14 
Deposition Author(s): Akutsu, M., Wagner, S.A., Beli, P.

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Funding Organization	Location	Grant Number
Emmy Noether Program	Germany	5342/1-1
SFB	Germany	SFB 1177
Marie Curie Career Integration Grant from the European Commission		630763
LOEWE program Ubiquitin Networks	Germany	--

Revision History  

• Version 1.0: 2018-02-14
  Type: Initial release
  
• Version 1.1: 2018-03-21
  Changes: Database references
• Version 1.2: 2019-03-13
  Changes: Data collection, Derived calculations
• Version 1.3: 2019-07-10
  Changes: Data collection
• Version 1.4: 2019-10-16
  Changes: Data collection
• Version 1.5: 2024-11-20
  Changes: Data collection, Database references, Structure summary