8YQL | pdb_00008yql

Roadblock domain from a Lokiarchaeota archaeon Roadblock-Longin protein in P31

• PDB DOI: https://doi.org/10.2210/pdb8YQL/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Promethearchaeum syntrophicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-19 Released: 2025-03-26 
• Deposition Author(s): Kitaoku, Y., Sitthisak, P., Robinson, R.C.
• Funding Organization(s): Simons Foundation, Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: in silico

Literature

Roadblock domain from a Lokiarchaeota archaeon Roadblock-Longin protein in P21

Sitthisak, P., Kitaoku, Y., Robinson, R.C.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 37.35 kDa 
• Atom Count: 2,632 
• Modeled Residue Count: 322 
• Deposited Residue Count: 327 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Roadblock domain in P31	A, B, C	109	Promethearchaeum syntrophicum	Mutation(s): 0  Gene Names: DSAG12_01965
UniProt
Find proteins for A0A5B9DBT7 (Promethearchaeum syntrophicum) Explore A0A5B9DBT7  Go to UniProtKB:  A0A5B9DBT7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.256 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.816	α = 90
b = 74.816	β = 90
c = 58.666	γ = 120

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-26 
Deposition Author(s): Kitaoku, Y., Sitthisak, P., Robinson, R.C.

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Funding Organization	Location	Grant Number
Simons Foundation	United States	GBMF9743
Japan Science and Technology	Japan	PMJCR19S5

Revision History  

• Version 1.0: 2025-03-26
  Type: Initial release