7ZHK

GPN-loop GTPase from Sulfolobus acidocaldarius open state (GDP)

• PDB DOI: https://doi.org/10.2210/pdb7ZHK/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Sulfolobus acidocaldarius
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-04-06 Released: 2023-10-25 
• Deposition Author(s): Korf, L., Essen, L.-O.
• Funding Organization(s): Volkswagen Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 

Literature

Archaeal GPN-loop GTPases involve a lock-switch-rock mechanism for GTP hydrolysis.

Korf, L., Ye, X., Vogt, M.S., Steinchen, W., Watad, M., van der Does, C., Tourte, M., Sivabalasarma, S., Albers, S.-V., Essen, L.-O.

(2023) mBio 14: e0085923-e0085923

• PubMed: 37962382 
• DOI: https://doi.org/10.1128/mbio.00859-23
• Primary Citation of Related Structures:  
  7ZHF, 7ZHK


• PubMed Abstract: 
  

  GPN-loop GTPases have been found to be crucial for eukaryotic RNA polymerase II assembly and nuclear trafficking. Despite their ubiquitous occurrence in eukaryotes and archaea, the mechanism by which these GTPases mediate their function is unknown. Our study on an archaeal representative from Sulfolobus acidocaldarius showed that these dimeric GTPases undergo large-scale conformational changes upon GTP hydrolysis, which can be summarized as a lock-switch-rock mechanism. The observed requirement of Sa GPN for motility appears to be due to its large footprint on the archaeal proteome.

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Organizational Affiliation: 

Department of Chemistry, Philipps University, Marburg, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 93.98 kDa 
• Atom Count: 6,114 
• Modelled Residue Count: 721 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase	A, B, C	274	Sulfolobus acidocaldarius	Mutation(s): 0  Gene Names: ATY89_00095, ATZ20_03140
UniProt
Find proteins for A0A0U2WWJ1 (Sulfolobus acidocaldarius) Explore A0A0U2WWJ1  Go to UniProtKB:  A0A0U2WWJ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	D [auth A], F [auth B], H [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.247 
• R-Value Work: 0.188 
• R-Value Observed: 0.191 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.689	α = 90
b = 141.878	β = 90
c = 100.239	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
PHASER	phasing
XDS	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-25 
Deposition Author(s): Korf, L., Essen, L.-O.

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Funding Organization	Location	Grant Number
Volkswagen Foundation	Germany	--

Revision History  

• Version 1.0: 2023-10-25
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Database references