Structure of PDB 6gkh Chain A

Receptor sequence

>6gkhA (length=685) Species: 10090 (Mus musculus)

ELQLRPYQMEVAQPALDGKNIIICLPTGSGKTRVAVYITKDHLDKKKQAS
ESGKVIVLVNKVMLAEQLFRKEFNPYLKKWYRIIGLSGDTQLKISFPEVV
KSYDVIISTAQILENSLLNLESGDDDGVQLSDFSLIIIDECHHTNKEAVY
NNIMRRYLKQKLRNNDLKKQNKPAIPLPQILGLTASPGVGAAKKQSEAEK
HILNICANLDAFTIKTVKENLGQLKHQIKEPCKKFVIADDTRENPFKEKL
LEIMASIQTYCQKSPMSDFGTQHYEQWAIQMEKKAAKDGNRKDRVCAEHL
RKYNEALQINDTIRMIDAYSHLETFYTDEKEKKFAVLNDKSLKLDETDEF
LMNLFFDNKKMLKKLAENPKYENEKLIKLRNTILEQFTRSEESSRGIIFT
KTRQSTYALSQWIMENAKFAEVGVKAHHLIGAGHSSEVKPMTQTEQKEVI
SKFRTGEINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARA
DESTYVLVTSSGSGVTEREIVNDFREKMMYKAINRVQNMKPEEYAHKILE
LQVQSILEKKMKVKRSIAKQYNDNPSLITLLCKNCSMLVCSGENIHVIEK
MHHVNMTPEFKGLYIVRENQTNGEIICKCGQAWGTMMVHKGLDLPCLKIR
NFVVNFKNNSPKKQYKKWVELPIRFPDLDYSEYCL

3D structure

• PDB: 6gkh Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis.
• Chain: A
• Resolution: 4.06 Å

Enzymatic activity

• Enzyme Commision number: 3.6.4.13: RNA helicase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	K451 E452 H759 T811 R843 M926 H927 N957 K983 K1002	K146 E147 H434 T486 R518 M601 H602 N622 K648 K667
BS02	rna	A	G393 T414 Q416 R606 K726 R728 G756 T790 V791 E924 V973 K1001	G88 T109 Q111 R301 K401 R403 G431 T465 V466 E599 V638 K666
BS03	ADP	A	Q308 L309 R310 G333 G335 K336 R338 D797 R824	Q3 L4 R5 G28 G30 K31 R33 D472 R499
BS04	ALF	A	K336 R822 R824	K31 R497 R499
BS05	ZN	A	C907 C962 C964	C582 C627 C629

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003723 RNA binding
• GO:0003724 RNA helicase activity
• GO:0003725 double-stranded RNA binding
• GO:0003727 single-stranded RNA binding
• GO:0004386 helicase activity
• GO:0005515 protein binding
• GO:0005524 ATP binding
• GO:0008270 zinc ion binding
• GO:0016787 hydrolase activity
• GO:0016887 ATP hydrolysis activity
• GO:0019904 protein domain specific binding
• GO:0038187 pattern recognition receptor activity
• GO:0042802 identical protein binding
• GO:0043021 ribonucleoprotein complex binding
• GO:0046872 metal ion binding

Biological Process

• GO:0002376 immune system process
• GO:0009615 response to virus
• GO:0016925 protein sumoylation
• GO:0032727 positive regulation of interferon-alpha production
• GO:0032728 positive regulation of interferon-beta production
• GO:0032755 positive regulation of interleukin-6 production
• GO:0032760 positive regulation of tumor necrosis factor production
• GO:0039530 MDA-5 signaling pathway
• GO:0045071 negative regulation of viral genome replication
• GO:0045087 innate immune response
• GO:0051259 protein complex oligomerization
• GO:0051607 defense response to virus
• GO:0060337 type I interferon-mediated signaling pathway
• GO:0060760 positive regulation of response to cytokine stimulus
• GO:0071360 cellular response to exogenous dsRNA
• GO:0098586 cellular response to virus
• GO:0140374 antiviral innate immune response

Cellular Component

• GO:0005634 nucleus
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion

External links

• PDB: RCSB:6gkh, PDBe:6gkh, PDBj:6gkh
• PDBsum: 6gkh
• PubMed: 30449722
• UniProt: Q8R5F7|IFIH1_MOUSE Interferon-induced helicase C domain-containing protein 1 (Gene Name=Ifih1)