9YY5 | pdb_00009yy5

Crystal structure of P. furiosus SRP54 NG domain G225E

• PDB DOI: https://doi.org/10.2210/pdb9YY5/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Pyrococcus furiosus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-10-28 Released: 2026-10-28 
• Deposition Author(s): Yang, M., Bruner, S.D.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Structure and Function

Yang, M., Brim, A.D., Long, L.F., Wu, G.C., Schlichting, G.M., Denard, C.A., Bruner, S.D.

(2026) ACS Omega 

• DOI: https://doi.org/10.1021/acsomega.6c06315

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 35.37 kDa 
• Atom Count: 2,621 
• Modeled Residue Count: 303 
• Deposited Residue Count: 316 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Signal recognition particle 54 kDa protein	A	316	Pyrococcus furiosus	Mutation(s): 1  Gene Names: srp54, PF1731 EC: 3.6.5.4
UniProt
Find proteins for Q8U070 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U070  Go to UniProtKB:  Q8U070

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.249	α = 90
b = 73.249	β = 90
c = 123.689	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-10-28 
Deposition Author(s): Yang, M., Bruner, S.D.

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Funding Organization	Location	Grant Number
Other government	United States	23L04

Revision History  

• Version 1.0: 2026-10-28
  Type: Initial release