3TZR | pdb_00003tzr

Structure of a Riboswitch-like RNA-ligand complex from the Hepatitis C Virus Internal Ribosome Entry Site

• PDB DOI: https://doi.org/10.2210/pdb3TZR/pdb
• NAKB: 3TZR

• Classification: RNA
• Organism(s): Hepacivirus hominis
• Mutation(s): No 


• Deposited: 2011-09-27 Released: 2012-03-21 
• Deposition Author(s): Dibrov, S.M., Ding, K., Brunn, N., Parker, M.A., Bergdahl, B.M., Wyles, D.L., Hermann, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free: 
  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

Structure of a Riboswitch in the Hepatitis C Virus Internal Ribosome Entry Site

Hermann, T., Dibrov, S., Ding, K., Brunn, N., Parker, M., Bergdahl, M., Wyles, D.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 12.23 kDa 
• Atom Count: 883 
• Modeled Residue Count: 36 
• Deposited Residue Count: 36 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(*CP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*UP*GP*UP*CP*UP*UP*CP*CP*C)-3'	A	20	Hepacivirus hominis

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP*UP*CP*GP*UP*GP*CP*AP*GP*CP*CP*UP*CP*GP*G)-3'	B	16	Hepacivirus hominis

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SS0	K [auth A]	(8R)-8-[(dimethylamino)methyl]-1-[3-(dimethylamino)propyl]-1,7,8,9-tetrahydrochromeno[5,6-d]imidazol-2-amine C18 H29 N5 O HTUXJUVSTFSWOD-CYBMUJFWSA-N
SO4	H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.21 Å
• R-Value Free:  0.238 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 32.054	α = 90
b = 33.582	β = 90
c = 81.046	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Dibrov, S.M., Ding, K., Brunn, N., Parker, M.A., Bergdahl, B.M., Wyles, D.L., Hermann, T.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description