3LRN: Human RIG-I CTD

Crystal structure of human RIG-I CTD bound to a 14 bp GC 5' ppp dsRNA. Determined by X-ray diffraction at 2.6 Å resolution. Released 2 Jun 2010.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 2,674
Mol. weight: 37.87 kDa
Ligands: ZN
Released: 2 Jun 2010

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

Secondary structure: helices and β-sheets

3LRN contains 12 α-helices and 22 β-strands across 2 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: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	806-810	5	1
β-strand	816-819	4	1
α-helix	820-822	3
β-strand	823-826	4	2
β-strand	830-833	4	2
α-helix	836-840	5
β-strand	842-853	12	2
β-strand	856-864	9	2
β-strand	872-879	8	2
β-strand	882-887	6	2
α-helix	889-891	3
β-strand	892-896	5	1
β-strand	902-903	2	1
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	2
α-helix	918	1

Chain B: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	806-810	5	3
β-strand	816-819	4	3
β-strand	823-826	4	4
β-strand	830-833	4	4
α-helix	837-841	5
β-strand	842-846	5	4
β-strand	858-864	7	4
β-strand	872-879	8	4
β-strand	882-887	6	4
α-helix	889-891	3
β-strand	892-896	5	3
β-strand	902-903	2	3
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	4
α-helix	918	1
α-helix	920-922	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable ATP-dependent RNA helicase DDX58	A, B	protein	121	Homo sapiens	O95786 (AlphaFold model)
RNA (5'-r((gtp)pgpcpgpcpgpcpgpcpgpcpgpcpc)-3')	C, D	RNA	14

Sequence of entity 1 (A, B), FASTA

>3LRN_1 Probable ATP-dependent RNA helicase DDX58 (chains A, B)
KENKKLLCRKCKALACYTADVRVIEESHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKI
FCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAE
M

Sequence of entity 2 (C, D), FASTA

>3LRN_2 RNA (5'-R(*(GTP)P*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3') (chains C, D)
GGCGCGCGCGCGCC

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

The Structural Basis of 5' Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain. Lu, C., Xu, H., Ranjith-Kumar, C.T. et al. Structure (2010) 18:1032-1043. DOI 10.1016/j.str.2010.05.007 · 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
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
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

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