2YKG: Probable ATP-dependent RNA helicase DDX58

Structural insights into RNA recognition by RIG-I. Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Oct 2011.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: HOMO SAPIENS
Chains: 3
Atoms: 5,523
Mol. weight: 86.26 kDa
Ligands: ZN
Released: 26 Oct 2011

Explore 2YKG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2YKG contains 31 α-helices and 24 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 A: 31 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	245-255	11
β-strand	260-263	4	1
α-helix	270-284	15
α-helix	286	1
β-strand	293-296	4	1
α-helix	300-313	14
β-strand	321-324	4	1
α-helix	334-339	6
β-strand	343-346	4	1
α-helix	348-356	9
α-helix	363-365	3
β-strand	368-372	5	1
α-helix	374-376	3
α-helix	382-395	14
β-strand	404-409	6	1
α-helix	420-433	14
β-strand	438-440	3	1
α-helix	446-452	7
β-strand	457-462	6	2
α-helix	464-466	3
α-helix	470-489	20
α-helix	493-495	3
α-helix	507-518	12
α-helix	531-557	27
α-helix	560-575	16
α-helix	581-591	11
α-helix	594-602	9
α-helix	604-606	3
α-helix	609-622	14
β-strand	630-633	4	2
α-helix	637-649	13
β-strand	658-659	2	2
β-strand	695-698	4	2
β-strand	711-715	5	2
β-strand	737-742	6	2
α-helix	745-768	24
α-helix	773-793	21
α-helix	795-801	7
β-strand	806-810	5	3
β-strand	816-819	4	3
α-helix	820-822	3
β-strand	823-826	4	4
β-strand	830-833	4	4
α-helix	838-840	3
β-strand	842-852	11	5
β-strand	857-864	8	5
β-strand	872-879	8	5
β-strand	882-887	6	5
α-helix	889-891	3
β-strand	892-896	5	3
β-strand	902-904	3	3
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	4
α-helix	918	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable ATP-dependent RNA helicase DDX58	A	protein	696	HOMO SAPIENS	O95786 (AlphaFold model)
5'-r(gpcpgpcpgpcpgpcpgpcp)-3'	C, D	RNA	10	HOMO SAPIENS

Sequence of entity 1 (A), FASTA

>2YKG_1 PROBABLE ATP-DEPENDENT RNA HELICASE DDX58 (chains A)
SEVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQ
KGKVVFFANQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQ
ILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLT
ASVGVGDAKTTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISD
KFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKD
EESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQR
FEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEG
NPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQC
NLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQ
TWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEDC
HYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKI
ESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK

Sequence of entity 2 (C, D), FASTA

>2YKG_2 5'-R(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP)-3' (chains C, D)
GCGCGCGCGC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structural Insights Into RNA Recognition by Rig-I. Luo, D., Ding, S.C., Vela, A. et al. Cell (2011) 147:409. DOI 10.1016/J.CELL.2011.09.023 · 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
9KU4 2.4 Å, Cryo-EM structure of E373A mutant RIG-I with 5'p-RNA
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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