9KTW | pdb_00009ktw

Cryo-EM structure of wild type RIG-I with 5'p-RNA

• PDB DOI: https://doi.org/10.2210/pdb9KTW/pdb
• EM Map EMD-62568: EMDB EMDataResource
• NAKB: 9KTW

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-12-03 Released: 2025-12-03 
• Deposition Author(s): Tan, Y.B., Luo, D.
• Funding Organization(s): Ministry of Education (MoE, Singapore)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Cryo-EM structure of wild type RIG-I with 5'p-RNA

Tan, Y.B., Luo, D.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 126.05 kDa 
• Atom Count: 6,254 
• Modeled Residue Count: 714 
• Deposited Residue Count: 985 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Antiviral innate immune response receptor RIG-I	A [auth B]	925	Homo sapiens	Mutation(s): 0  Gene Names: RIGI, DDX58 EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O95786 (Homo sapiens) Explore O95786  Go to UniProtKB:  O95786
PHAROS:  O95786 GTEx:  ENSG00000107201

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'p-RNA (60-MER)	B [auth C]	60	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-03 
Deposition Author(s): Tan, Y.B., Luo, D.

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Funding Organization	Location	Grant Number
Ministry of Education (MoE, Singapore)	Singapore	MOE AcRF Tier 1 award RT22/23

Revision History  

• Version 1.0: 2025-12-03
  Type: Initial release