2QFD: Regulatory domain of human RIG-I with bound Hg

Crystal structure of the regulatory domain of human RIG-I with bound Hg. Determined by X-ray diffraction at 2.7 Å resolution. Released 12 Feb 2008.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 10
Atoms: 10,092
Mol. weight: 170.54 kDa
Ligands: HG
Released: 12 Feb 2008

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

Secondary structure: helices and β-sheets

2QFD contains 56 α-helices and 111 β-strands across 10 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: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	807-810	4	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	838-840	3
β-strand	842-846	5	3
β-strand	856-864	9	3
β-strand	872-879	8	3
β-strand	882-887	6	3
α-helix	889-891	3
β-strand	892-895	4	1
β-strand	902-904	3	1
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	2
α-helix	918	1
α-helix	920-922	3

Chain B: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	807-810	4	4
β-strand	816-819	4	4
α-helix	820-822	3
β-strand	823-826	4	5
β-strand	830-833	4	5
α-helix	838-840	3
β-strand	842-846	5	6
β-strand	857-864	8	6
β-strand	872-879	8	6
β-strand	882-887	6	6
α-helix	889-891	3
β-strand	892-895	4	4
β-strand	902-904	3	4
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	5
α-helix	918	1

Chain C: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	806-810	5	7
β-strand	816-819	4	7
α-helix	820-822	3
β-strand	823-826	4	8
β-strand	830-833	4	8
α-helix	836-839	4
β-strand	842-845	4	9
β-strand	857-864	8	9
β-strand	872-879	8	9
β-strand	882-887	6	9
α-helix	889-891	3
β-strand	892-896	5	7
β-strand	902-903	2	7
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	8
α-helix	918	1

Chain D: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	807-810	4	4
β-strand	816-819	4	4
β-strand	823-826	4	10
β-strand	830-833	4	10
α-helix	836-839	4
β-strand	842-846	5	11
β-strand	857-864	8	11
β-strand	872-879	8	11
β-strand	882-887	6	11
α-helix	889-891	3
β-strand	892-895	4	4
β-strand	902-904	3	4
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	10
α-helix	918	1

Chain E: 4 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	12
β-strand	830-833	4	12
α-helix	836-839	4
β-strand	842-843	2	13
β-strand	857-864	8	13
β-strand	872-878	7	13
β-strand	883-887	5	13
α-helix	889-891	3
β-strand	892-896	5	1
β-strand	902-904	3	1
α-helix	908-910	3
β-strand	917	1	12

Chain F: 7 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	807-810	4	14
β-strand	818-819	2	14
α-helix	820-822	3
β-strand	823-826	4	15
β-strand	830-833	4	15
α-helix	836-839	4
β-strand	842-846	5	16
α-helix	847	1
β-strand	852	1	16
β-strand	857-864	8	16
β-strand	872-879	8	16
β-strand	882-887	6	16
α-helix	889-891	3
β-strand	892-895	4	14
β-strand	902-903	2	14
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	15
α-helix	918	1

Chain G: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	807-810	4	17
β-strand	816-819	4	17
α-helix	820-822	3
β-strand	823-826	4	18
β-strand	830-833	4	18
α-helix	836-839	4
β-strand	842-846	5	19
β-strand	857-864	8	19
β-strand	872-879	8	19
β-strand	882-887	6	19
α-helix	889-891	3
β-strand	892-895	4	17
β-strand	902-904	3	17
α-helix	908-910	3
β-strand	916-917	2	18
α-helix	918	1

Chain H: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	807-810	4	20
β-strand	816-819	4	20
α-helix	820-822	3
β-strand	823-826	4	21
β-strand	830-833	4	21
α-helix	839-841	3
β-strand	842-846	5	22
β-strand	857-864	8	22
β-strand	872-878	7	22
β-strand	883-887	5	22
α-helix	889-891	3
β-strand	892-895	4	20
β-strand	902-903	2	20
α-helix	908-910	3
α-helix	916	1
β-strand	917	1	21
α-helix	918	1

2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable ATP-dependent RNA helicase DDX58	A, B, C, D, E, F, G, H, I, J	protein	145	Homo sapiens	O95786 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J), FASTA

>2QFD_1 Probable ATP-dependent RNA helicase DDX58 (chains A, B, C, D, E, F, G, H, I, J)
MGSSHHHHHHSSGLVPRGSHMDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKE
CFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATG
VQTLYSKWKDFHFEKIPFDPAEMSK

Ligands and cofactors

ID	Name	Formula	Copies
HG	Mercury (II) ion	Hg	10

Primary citation

The C-Terminal Regulatory Domain Is the RNA 5'-Triphosphate Sensor of RIG-I. Cui, S., Eisenacher, K., Kirchhofer, A. et al. Mol Cell (2008) 29:169-179. DOI 10.1016/j.molcel.2007.10.032 · 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
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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