4P4H: Probable ATP-dependent RNA helicase DDX58

Caught-in-action signaling complex of RIG-I 2CARD domain and MAVS CARD domain. Determined by X-ray diffraction at 3.4 Å resolution. Released 30 Jul 2014.

Method: X-ray diffraction
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 21
Atoms: 21,711
Mol. weight: 334.39 kDa
Released: 30 Jul 2014

Explore 4P4H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4P4H contains 187 α-helices and 35 β-strands across 21 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: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	2-11	10
α-helix	13-19	7
α-helix	22-25	4
α-helix	35-48	14
α-helix	50-63	14
α-helix	69-80	12
α-helix	86-91	6
α-helix	95-99	5
α-helix	101-117	17
α-helix	120-127	8
α-helix	128-130	3
α-helix	133-146	14
α-helix	148-160	13
α-helix	167-177	11

Chain B: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	13-19	7
α-helix	22-24	3
α-helix	26-29	4
α-helix	35-48	14
α-helix	50-62	13
α-helix	69-80	12
α-helix	85-91	7
α-helix	95-99	5
α-helix	101-109	9
α-helix	111-117	7
α-helix	120-123	4
α-helix	133-146	14
α-helix	148-161	14
α-helix	167-176	10

Chain C: 12 helices, 0 β-strands

Element	Residues	Length
α-helix	6-11	6
α-helix	13-19	7
α-helix	22-29	8
α-helix	35-48	14
α-helix	50-61	12
α-helix	69-80	12
α-helix	86-91	6
α-helix	95-117	23
α-helix	120-127	8
α-helix	133-146	14
α-helix	148-161	14
α-helix	167-177	11

Chain D: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	13-19	7
α-helix	22-29	8
α-helix	38-48	11
α-helix	50-62	13
α-helix	69-80	12
α-helix	85-91	7
α-helix	95-99	5
α-helix	101-109	9
α-helix	113-116	4
α-helix	120-123	4
α-helix	126-129	4
α-helix	133-145	13
α-helix	148-160	13
α-helix	167-174	8

Chain E: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	2-11	10
α-helix	13-19	7
α-helix	22-25	4
α-helix	35-48	14
α-helix	50-63	14
α-helix	69-80	12
α-helix	86-91	6
α-helix	95-99	5
α-helix	101-109	9
α-helix	111-117	7
α-helix	120-127	8
α-helix	128-130	3
α-helix	133-146	14
α-helix	148-160	13
α-helix	167-177	11

Chain F: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	13-19	7
α-helix	22-29	8
α-helix	35-48	14
α-helix	50-62	13
α-helix	69-80	12
α-helix	85-91	7
α-helix	95-99	5
α-helix	101-109	9
α-helix	111-117	7
α-helix	120-123	4
α-helix	133-146	14
α-helix	148-161	14
α-helix	167-176	10

Chain G: 13 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	13-19	7
α-helix	22-29	8
α-helix	35-48	14
α-helix	50-61	12
α-helix	69-79	11
α-helix	86-91	6
α-helix	95-109	15
α-helix	111-117	7
α-helix	120-127	8
α-helix	133-146	14
α-helix	148-161	14
α-helix	167-177	11

Chain H: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	3-11	9
α-helix	13-19	7
α-helix	22-29	8
α-helix	38-48	11
α-helix	50-62	13
α-helix	69-80	12
α-helix	85-91	7
α-helix	95-99	5
α-helix	101-109	9
α-helix	111-117	7
α-helix	120-123	4
α-helix	126-129	4
α-helix	133-145	13
α-helix	148-161	14
α-helix	167-175	9

9 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	protein	205	Homo sapiens	O95786 (AlphaFold model)
Mitochondrial antiviral-signaling protein	I, J, K, L, M, N, O, P	protein	108	Homo sapiens	Q7Z434 (AlphaFold model)
Ubiquitin-60S ribosomal protein L40	S, T, U, W, X	protein	79	Homo sapiens	P62987 (AlphaFold model)

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

>4P4H_1 Probable ATP-dependent RNA helicase DDX58 (chains A, B, C, D, E, F, G, H)
GPGAMTTEQRRSLQAFQDYIRKTLDPTYILSYMAPWFREEEVQYIQAEKNNKGPMAAATL
FLKFLLELQEEGWFRGFLDALDHAGYSGLYEAIESWDFKKIEKLEEYRLLLKRLQPEFKT
RIIPTDIISDLSECLINQECEEILQICSTKGMMAGAEKLVECLLRSDKENWPKTLKLALE
KERNKFSELWIVEKGIKDVETEDLE

Sequence of entity 2 (I, J, K, L, M, N, O, P), FASTA

>4P4H_2 Mitochondrial antiviral-signaling protein (chains I, J, K, L, M, N, O, P)
GSGTGSTGSMPFAEDKTYKYICRNFSNFCNVKVVKILPYLPCLTARDQDRLRATCTLSGN
RDTLWHLFNTLQRRPGWVEYFIAALRGCKLVDLADEVASVYQSYQPRT

Sequence of entity 3 (S, T, U, W, X), FASTA

>4P4H_3 Ubiquitin-60S ribosomal protein L40 (chains S, T, U, W, X)
GPGMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLS
DYNIQKESTLHLVLRLRGG

Primary citation

Molecular Imprinting as a Signal-Activation Mechanism of the Viral RNA Sensor RIG-I. Wu, B., Peisley, A., Tetrault, D. et al. Mol Cell (2014) 55:511-523. DOI 10.1016/j.molcel.2014.06.010 · 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

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