9KU4: E373A mutant RIG-I with 5'p-RNA

Cryo-EM structure of E373A mutant RIG-I with 5'p-RNA. Determined by electron microscopy at 2.4 Å resolution. Released 3 Dec 2025.

Method: Electron microscopy
Resolution: 2.4 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 6,250
Mol. weight: 125.99 kDa
Ligands: ZN
Released: 3 Dec 2025

Explore 9KU4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9KU4 contains 33 α-helices and 28 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 33 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	241-244	4
α-helix	245-255	11
β-strand	260-263	4	1
α-helix	270-283	14
α-helix	286	1
β-strand	293-296	4	1
α-helix	300-314	15
β-strand	321-324	4	1
α-helix	326-328	3
α-helix	334-339	6
β-strand	343-346	4	1
α-helix	348-357	10
β-strand	368-372	5	1
α-helix	374-376	3
α-helix	382-394	13
β-strand	404-409	6	1
α-helix	420-433	14
β-strand	438-440	3	1
α-helix	446-452	7
α-helix	455-456	2
β-strand	457-462	6	2
α-helix	470-489	20
α-helix	493-495	3
α-helix	507-520	14
α-helix	528-557	30
α-helix	560-575	16
α-helix	581-601	21
α-helix	604-606	3
α-helix	609-624	16
β-strand	630-633	4	2
α-helix	637-649	13
β-strand	658-661	4	2
α-helix	675-684	10
β-strand	685	1	3
β-strand	691	1	3
β-strand	693-696	4	2
α-helix	698-700	3
β-strand	711-715	5	2
α-helix	721-728	8
β-strand	737-742	6	2
α-helix	745-768	24
α-helix	773-793	21
β-strand	802	1	4
β-strand	806-810	5	5
β-strand	816-819	4	5
α-helix	820-822	3
β-strand	823-826	4	6
β-strand	830-833	4	6
α-helix	838-840	3
β-strand	842-845	4	6
α-helix	859-860	2
β-strand	861-864	4	6
β-strand	872-879	8	6
β-strand	882-887	6	6
α-helix	889-891	3
β-strand	892-896	5	5
β-strand	902-903	2	5
β-strand	913	1	4
β-strand	916-917	2	6
α-helix	918	1
α-helix	920-922	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Antiviral innate immune response receptor RIG-I	B	protein	925	Homo sapiens	O95786 (AlphaFold model)
RNA (60-mer)	C	RNA	60	synthetic construct

Sequence of entity 1 (B), FASTA

>9KU4_1 Antiviral innate immune response receptor RIG-I (chains B)
MTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMEAATLFLKF
LLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKTRIIP
TDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALEKERN
KFSELWIVEKGIKDVETEDLEDKMETSDIQIFYQEDPECQNLSENSCPPSEVSDTNLYSP
FKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQI
PVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTI
PSLSIFTLMIFDACHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNT
DEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMR
DTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFL
YTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESV
SRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGI
LTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGN
VIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKI
LHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKE
CFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATG
VQTLYSKWKDFHFEKIPFDPAEMSK

Sequence of entity 2 (C), FASTA

>9KU4_2 RNA (60-MER) (chains C)
GGGACGCUGACCCAGAAGAUCUACUAGAAAUAGUAGAUCUUCUGGGUCAGCGUCCCUUUU

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Local activation of mutant RIG-I by short noncoding Y-RNA in the kidney triggers lethal nephritis. Satoh, S., Tan, Y.B., Heil, B. et al. Sci Immunol (2025) 10:eadx1135-eadx1135. DOI 10.1126/sciimmunol.adx1135 · PubMed

Other PDB entries of the same protein (UniProt O95786 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7BAH 1.89 Å, Structure of RIG-I CTD bound to OH-RNA
7MK1 1.9 Å, Structure of a protein-modified aptamer complex
3LRR 2.15 Å, Crystal structure of human RIG-I CTD bound to a 12 bp AU rich 5' ppp dsRNA
3OG8 2.4 Å, Crystal structure of human RIG-I CTD bound to a 14-bp blunt-ended dsRNA
2YKG 2.5 Å, Structural insights into RNA recognition by RIG-I
3ZD7 2.5 Å, Snapshot 3 of RIG-I scanning on RNA duplex
3NCU 2.55 Å, Structural and functional insights into pattern recognition by the innate immune…
4BPB 2.58 Å, Structural insights into RNA recognition by rig-I
3LRN 2.6 Å, Crystal structure of human RIG-I CTD bound to a 14 bp GC 5' ppp dsRNA
9KTW 2.6 Å, Cryo-EM structure of wild type RIG-I with 5'p-RNA
5F9F 2.6 Å, Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA
2QFD 2.7 Å, Crystal structure of the regulatory domain of human RIG-I with bound Hg

Browse structure collections

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