5F9F: RIG-I helicase-RD

Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA. Determined by X-ray diffraction at 2.6 Å resolution. Released 13 Jan 2016.

Method

X-ray diffraction

Resolution

2.6 Å

Organisms

Homo sapiens, synthetic construct

Chains

12

Atoms

34,918

Mol. weight

525.58 kDa

Ligands

BU3, ETF, MG, ZN

Released

13 Jan 2016

Explore 5F9F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5F9F contains 199 α-helices and 157 β-strands across 6 chains. 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: 36 helices, 24 β-strands

Molecules and chains

>5F9F_1 Probable ATP-dependent RNA helicase DDX58 (chains A, C, E, G, I, K)
SVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQK
GKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQI
LVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTA
SVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDK
FKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDE
ESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRF
EEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGN
PKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCN
LVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQT
WDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECH
YTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIE
SFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK

>5F9F_2 RNA (5'-R(*GP*AP*AP*UP*AP*UP*AP*AP*UP*AP*GP*UP*GP*AP*UP*AP*UP*UP*AP*UP*AP*UP*UP*C)-3') (chains B, D, F, H, J, L)
GAAUAUAAUAGUGAUAUUAUAUUC

Ligands and cofactors

Primary citation

Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Devarkar, S.C., Wang, C., Miller, M.T. et al. Proc Natl Acad Sci U S A (2016) 113:596-601. DOI 10.1073/pnas.1515152113 · PubMed

Related structures

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
• 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
• 2QFD 2.7 Å, Crystal structure of the regulatory domain of human RIG-I with bound Hg

Browse structure collections

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