9TKV | pdb_00009tkv

Structure of duck RIG-I (delta CARDS) bound to 31-mer RNA mismatched hairpin with 5'pppG-C blunt end, mimicking the influenza B virus vRNA promoter (panhandle).

PDB DOI: https://doi.org/10.2210/pdb9TKV/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Anas platyrhynchos, Influenza B virus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-12-10 Released: 2025-12-31
Deposition Author(s): Cusack, S., Ivanov, I.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.49 Å
R-Value Free:
0.191 (Depositor), 0.192 (DCC)
R-Value Work:
0.147 (Depositor), 0.147 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

High resolution crystal structures of duck RIG-I and chicken LGP2 bound to non-canonical duplexes mimicking the influenza virus vRNA promoter (panhandle).

Cusack, S., Ivanov, I., Uchikawa, E.

To be published.

Macromolecule Content

Total Structure Weight: 89.8 kDa
Atom Count: 7,313
Modeled Residue Count: 705
Deposited Residue Count: 722
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA helicase	A	692	Anas platyrhynchos	Mutation(s): 0 Gene Names: RIG-I EC: 3.6.4.13
UniProt
Find proteins for D3TI84 (Anas platyrhynchos) Explore D3TI84 Go to UniProtKB: D3TI84
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	D3TI84
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
31-mer RNA hairpin with 5'pppG-C blunt end mimicking the influenza B virus vRNA promoter (panhandle)	B [auth R]	30	Influenza B virus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download Ideal Coordinates CCD File SDF format, chain J [auth R] MOL2 format, chain J [auth R] mmCIF format, chain J [auth R]	J [auth R]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain J [auth R] Interactions & Density Focus chain J [auth R]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth R] MOL2 format, chain I [auth R] mmCIF format, chain I [auth R]	I [auth R]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth R] Interactions & Density Focus chain I [auth R]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain H [auth R] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth R] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth R]	D [auth A], G [auth A], H [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth R] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth R]