5E3H: RNA Recognition and Activation of RIG-I

Structural Basis for RNA Recognition and Activation of RIG-I. Determined by X-ray diffraction at 2.7 Å resolution. Released 18 Nov 2015.

Method

X-ray diffraction

Resolution

2.7 Å

Organisms

Homo sapiens, synthetic construct

Chains

3

Atoms

5,517

Mol. weight

89.27 kDa

Ligands

ZN, MG, ADP, BEF

Released

18 Nov 2015

Explore 5E3H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E3H contains 34 α-helices and 22 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: 34 helices, 22 β-strands

Molecules and chains

>5E3H_1 Probable ATP-dependent RNA helicase DDX58 (chains A)
SVSDTNLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQK
GKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQI
LVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTA
SVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDK
FKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDE
ESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRF
EEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGN
PKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCN
LVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQT
WDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECH
YTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIE
SFVVEDIATGVQTLYSKWKDFHFEKIPFDPAEMSK

>5E3H_2 RNA (5'-R(*CP*GP*AP*CP*GP*CP*UP*AP*GP*CP*GP*U)-3') (chains B, C)
CGACGCUAGCGUCG

Ligands and cofactors

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

Primary citation

Structural basis of RNA recognition and activation by innate immune receptor RIG-I. Jiang, F., Ramanathan, A., Miller, M.T. et al. Nature (2011) 479:423-427. DOI 10.1038/nature10537 · 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
• 5F9F 2.6 Å, Crystal structure of RIG-I helicase-RD in complex with 24-mer blunt-end hairpin RNA

Browse structure collections

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