6ZT0 | pdb_00006zt0

Crystal structure of the Eiger TNF domain/Grindelwald extracellular domain complex

• PDB DOI: https://doi.org/10.2210/pdb6ZT0/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-07-17 Released: 2021-03-03 
• Deposition Author(s): Palmerini, V., Cecatiello, V., Pasqualato, S., Mapelli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Drosophila TNFRs Grindelwald and Wengen bind Eiger with different affinities and promote distinct cellular functions.

Palmerini, V., Monzani, S., Laurichesse, Q., Loudhaief, R., Mari, S., Cecatiello, V., Olieric, V., Pasqualato, S., Colombani, J., Andersen, D.S., Mapelli, M.

(2021) Nat Commun 12: 2070-2070

• PubMed: 33824334 
• DOI: https://doi.org/10.1038/s41467-021-22080-9
• Primary Citation Related Structures: 
  6ZSY, 6ZSZ, 6ZT0


• PubMed Abstract: 
  

  The Drosophila tumour necrosis factor (TNF) ligand-receptor system consists of a unique ligand, Eiger (Egr), and two receptors, Grindelwald (Grnd) and Wengen (Wgn), and therefore provides a simple system for exploring the interplay between ligand and receptors, and the requirement for Grnd and Wgn in TNF/Egr-mediated processes. Here, we report the crystallographic structure of the extracellular domain (ECD) of Grnd in complex with Egr, a high-affinity hetero-hexameric assembly reminiscent of human TNF:TNFR complexes. We show that ectopic expression of Egr results in internalisation of Egr:Grnd complexes in vesicles, a step preceding and strictly required for Egr-induced apoptosis. We further demonstrate that Wgn binds Egr with much reduced affinity and is localised in intracellular vesicles that are distinct from those containing Egr:Grnd complexes. Altogether, our data provide insight into ligand-mediated activation of Grnd and suggest that distinct affinities of TNF ligands for their receptors promote different and non-redundant cellular functions.

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Organizational Affiliation: 
• IEO, European Institute of Oncology IRCCS, Milan, Italy.
Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen O, Denmark.
Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical University of Copenhagen, Copenhagen N, Denmark.
Paul Scherrer Institute, Villigen-PSI, Switzerland.
IEO, European Institute of Oncology IRCCS, Milan, Italy. [e-mail].
Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen O, Denmark. [e-mail].
Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical University of Copenhagen, Copenhagen N, Denmark. [e-mail].
Department of Biology, Faculty of Science, University of Copenhagen, Copenhagen O, Denmark. [e-mail].
Novo Nordisk Foundation Center for Stem Cell Research, Faculty of Health and Medical University of Copenhagen, Copenhagen N, Denmark. [e-mail].
IEO, European Institute of Oncology IRCCS, Milan, Italy. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Macromolecule Content 

• Total Structure Weight: 22.65 kDa 
• Atom Count: 1,684 
• Modeled Residue Count: 192 
• Deposited Residue Count: 195 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein eiger	A	143	Drosophila melanogaster	Mutation(s): 0  Gene Names: egr, Darth, CG12919
UniProt
Find proteins for Q8MUJ1 (Drosophila melanogaster) Explore Q8MUJ1  Go to UniProtKB:  Q8MUJ1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein grindelwald	B [auth AAAA]	52	Drosophila melanogaster	Mutation(s): 0  Gene Names: grnd, CG10176
UniProt
Find proteins for Q9VJ83 (Drosophila melanogaster) Explore Q9VJ83  Go to UniProtKB:  Q9VJ83

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.707	α = 90
b = 78.707	β = 90
c = 57.657	γ = 120

Software Package:

Software Name	Purpose
autoPROC	data collection
PHENIX	refinement
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-03-03 
Deposition Author(s): Palmerini, V., Cecatiello, V., Pasqualato, S., Mapelli, M.

Revision History  

• Version 1.0: 2021-03-03
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Derived calculations
• Version 1.2: 2021-10-13
  Changes: Data collection, Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary