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.

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
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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-R(CPGPAPGPGPAPAPCPUPAPCPUPGPUPCPUPUPCPCPC)-3'	A	20	Hepacivirus hominis
Sequence Annotations Expand
Reference Sequence LOADING

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(GPGPUPCPGPUPGPCPAPGPCPCPUPCPGPG)-3'	B	16	Hepacivirus hominis
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SS0 Query on SS0 Download Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	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		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	H [auth A], I [auth A], J [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain L [auth B]

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

Revision History (Full details and data files)

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

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