3ZD7: Snapshot 3 of RIG-I scanning on RNA duplex

Snapshot 3 of RIG-I scanning on RNA duplex. Determined by X-ray diffraction at 2.5 Å resolution. Released 7 Aug 2013.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: HOMO SAPIENS, SYNTHETIC CONSTRUCT
Chains: 3
Atoms: 5,369
Mol. weight: 86.64 kDa
Ligands: ZN, ADP, MG
Released: 7 Aug 2013

Explore 3ZD7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ZD7 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	242-244	3
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	300-313	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	446-449	4
α-helix	456	1
β-strand	457-462	6	2
α-helix	470-489	20
α-helix	493-495	3
α-helix	507-517	11
α-helix	534-557	24
α-helix	560-577	18
α-helix	583-602	20
α-helix	604-606	3
α-helix	609-624	16
β-strand	630-633	4	2
α-helix	637-647	11
α-helix	651-653	3
β-strand	658-660	3	2
β-strand	695-698	4	2
α-helix	706-708	3
β-strand	711-715	5	2
β-strand	737-742	6	2
α-helix	745-769	25
α-helix	773-792	20
β-strand	807-810	4	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	837-840	4
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	892-895	4	3
β-strand	902-903	2	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)
RNA duplex	C, D	RNA	10	SYNTHETIC CONSTRUCT

Sequence of entity 1 (A), FASTA

>3ZD7_1 PROBABLE ATP-DEPENDENT RNA HELICASE DDX58 (chains A)
SEVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQ
KGKVVFFANQIPVYEQNKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQ
ILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLT
ASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISD
KFKYIIAQLMRDTESLAKRICKDLENLSQSQNREFGTQKYEQWIVTVQKACMVFQMPDKD
EESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQR
FEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEG
NPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILILTSVADEGIDIAQC
NLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQ
TWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEDC
HYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKI
ESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK

Sequence of entity 2 (C, D), FASTA

>3ZD7_2 RNA DUPLEX (chains C, D)
GCGCGCGCGC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1

Primary citation

Defining the Functional Determinants for RNA Surveillance by Rig-I. Kohlway, A., Luo, D., Rawling, D.C. et al. EMBO Rep (2013) 14:772. DOI 10.1038/EMBOR.2013.108 · 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
2YKG 2.5 Å, Structural insights into RNA recognition by RIG-I
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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