9LOV | pdb_00009lov

LGP2:MDA5:dsRNA filament

PDB DOI: https://doi.org/10.2210/pdb9LOV/pdb
EM Map EMD-63261: EMDB EMDataResource

Classification: IMMUNE SYSTEM/RNA
Organism(s): uncultured archaeon, Homo sapiens
Expression System: Spodoptera frugiperda, Escherichia coli
Mutation(s): Yes

Deposited: 2025-01-23 Released: 2026-01-28
Deposition Author(s): Kurihara, N., Isayama, Y., Nureki, O., Kato, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.07 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

LGP2:MDA5:dsRNA filament

Kurihara, N., Isayama, Y., Nureki, O., Kato, K.

To be published.

Macromolecule Content

Total Structure Weight: 277.1 kDa
Atom Count: 17,978
Modeled Residue Count: 2,080
Deposited Residue Count: 2,246
Unique protein chains: 2
Unique nucleic acid chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent RNA helicase DHX58	C [auth A]	678	Homo sapiens	Mutation(s): 1 Gene Names: DHX58, D11LGP2E, LGP2 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q96C10 (Homo sapiens) Explore Q96C10 Go to UniProtKB: Q96C10
PHAROS: Q96C10 GTEx: ENSG00000108771
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96C10
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Interferon-induced helicase C domain-containing protein 1	D [auth B], E [auth C]	739	Homo sapiens	Mutation(s): 3 Gene Names: IFIH1, MDA5, RH116 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYX4 (Homo sapiens) Explore Q9BYX4 Go to UniProtKB: Q9BYX4
PHAROS: Q9BYX4 GTEx: ENSG00000115267
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BYX4
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (45-MER)	A [auth Y]	45	uncultured archaeon
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (45-MER)	B [auth X]	45	uncultured archaeon
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C]	F [auth A], I [auth B], L [auth C]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C]	G [auth A], J [auth B], M [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C]	H [auth A], K [auth B], N [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C]