7EZD | pdb_00007ezd

Thorarchaeota Rab co-crystallized with GTP gamma-S

• PDB DOI: https://doi.org/10.2210/pdb7EZD/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Candidatus Thorarchaeota archaeon SMTZ1-45
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-01 Released: 2022-06-08 
• Deposition Author(s): Robinson, R.C., Tran, L.T.
• Funding Organization(s): Japan Science and Technology, Japan Society for the Promotion of Science (JSPS), Moore and Simons Foundations

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free: 
  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 

Starting Model: experimental

Literature

The eukaryotic-like characteristics of small GTPase, roadblock and TRAPPC3 proteins from Asgard archaea

Tran, L.T., Akil, C., Senju, Y., Robinson, R.C.

(2024) Commun Biol 7: 273

• DOI: https://doi.org/10.1038/s42003-024-05888-1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 42.76 kDa 
• Atom Count: 3,312 
• Modeled Residue Count: 346 
• Deposited Residue Count: 364 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chains: A,B	A, B	182	Candidatus Thorarchaeota archaeon SMTZ1-45	Mutation(s): 0  Gene Names: AM325_13980

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSP	D [auth B]	5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE C10 H16 N5 O13 P3 S XOFLBQFBSOEHOG-UUOKFMHZSA-N
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.76 Å
• R-Value Free:  0.189 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.656	α = 90
b = 68.656	β = 90
c = 66.579	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-08 
Deposition Author(s): Robinson, R.C., Tran, L.T.

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Funding Organization	Location	Grant Number
Japan Science and Technology	Japan	JPMJCR19S5
Japan Society for the Promotion of Science (JSPS)	Japan	JP20H00476
Moore and Simons Foundations	United States	GBMF9743

Revision History  

• Version 1.0: 2022-06-08
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description
• Version 1.2: 2025-01-29
  Changes: Database references, Structure summary