7OD9 | pdb_00007od9

Crystal structure of activated CheY fused to the C-terminal domain of CheF

• PDB DOI: https://doi.org/10.2210/pdb7OD9/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Methanococcus maripaludis X1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-04-29 Released: 2022-04-27 
• Deposition Author(s): Altegoer, F., Weiland, P., Bange, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.307 (Depositor), 0.308 (DCC) 
• R-Value Work: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

Literature

Structural insights into the mechanism of archaellar rotational switching.

Altegoer, F., Quax, T.E.F., Weiland, P., Nussbaum, P., Giammarinaro, P.I., Patro, M., Li, Z., Oesterhelt, D., Grininger, M., Albers, S.V., Bange, G.

(2022) Nat Commun 13: 2857-2857

• PubMed: 35606361 
• DOI: https://doi.org/10.1038/s41467-022-30358-9
• Primary Citation Related Structures: 
  7OD9, 7OVP


• PubMed Abstract: 
  

  Signal transduction via phosphorylated CheY towards the flagellum and the archaellum involves a conserved mechanism of CheY phosphorylation and subsequent conformational changes within CheY. This mechanism is conserved among bacteria and archaea, despite substantial differences in the composition and architecture of archaellum and flagellum, respectively. Phosphorylated CheY has higher affinity towards the bacterial C-ring and its binding leads to conformational changes in the flagellar motor and subsequent rotational switching of the flagellum. In archaea, the adaptor protein CheF resides at the cytoplasmic face of the archaeal C-ring formed by the proteins ArlCDE and interacts with phosphorylated CheY. While the mechanism of CheY binding to the C-ring is well-studied in bacteria, the role of CheF in archaea remains enigmatic and mechanistic insights are absent. Here, we have determined the atomic structures of CheF alone and in complex with activated CheY by X-ray crystallography. CheF forms an elongated dimer with a twisted architecture. We show that CheY binds to the C-terminal tail domain of CheF leading to slight conformational changes within CheF. Our structural, biochemical and genetic analyses reveal the mechanistic basis for CheY binding to CheF and allow us to propose a model for rotational switching of the archaellum.

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Organizational Affiliation: 
• Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Karl-von-Frisch-Straße 14, 35043, Marburg, Germany. [e-mail].
Heinrich-Heine University Düsseldorf, Institute of Microbiology, Universitätsstraße 1, 40225, Düsseldorf, Germany. [e-mail].
Archaeal virus-host interactions, Faculty for Biology, University of Freiburg, Schaenzlestrasse 1, 79104, Freiburg, Germany.
Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Karl-von-Frisch-Straße 14, 35043, Marburg, Germany.
Max-Planck Institute for Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
Goethe University Frankfurt, Institute of Organic Chemistry and Chemical Biology and Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Straße 15, 60438, Frankfurt am Main, Germany.
Philipps-University Marburg, Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Karl-von-Frisch-Straße 14, 35043, Marburg, Germany. [e-mail].
Max-Planck Institute for terrestrial Microbiology, Karl-von-Frisch-Straße 10, 35043, Marburg, Germany. [e-mail].

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 56.79 kDa 
• Atom Count: 3,374 
• Modeled Residue Count: 422 
• Deposited Residue Count: 514 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Response regulator receiver protein	A [auth B], B [auth A]	142	Methanococcus maripaludis X1	Mutation(s): 0  Gene Names: GYY_05385
UniProt
Find proteins for G0H061 (Methanococcus maripaludis X1) Explore G0H061  Go to UniProtKB:  G0H061

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
C-terminal domain of CheF from Methanococcus maripaludis	C, D [auth F]	115	Methanococcus maripaludis X1	Mutation(s): 0  Gene Names: GYY_05390
UniProt
Find proteins for G0H062 (Methanococcus maripaludis X1) Explore G0H062  Go to UniProtKB:  G0H062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BEF (Subject of Investigation/LOI)	F [auth B], H [auth A]	BERYLLIUM TRIFLUORIDE ION Be F3 OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG (Subject of Investigation/LOI)	E [auth B], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.307 (Depositor), 0.308 (DCC) 
• R-Value Work:  0.249 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.29	α = 90
b = 70.87	β = 91.603
c = 59.82	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-04-27 
Deposition Author(s): Altegoer, F., Weiland, P., Bange, G.

Revision History  

• Version 1.0: 2022-04-27
  Type: Initial release
  
• Version 1.1: 2022-06-08
  Changes: Database references
• Version 1.2: 2024-01-31
  Changes: Data collection, Refinement description