Structure of PDB 6gkm Chain A

Receptor sequence

>6gkmA (length=689) Species: 10090 (Mus musculus)

LQLRPYQMEVAQPALDGKNIIICLPTGSGKTRVAVYITKDHLDKKKQASE
SGKVIVLVNKVMLAEQLFRKEFNPYLKKWYRIIGLSGDTQLKISFPEVVK
SYDVIISTAQILENSLLNLESGDDDGVQLSDFSLIIIDECHHTNKEAVYN
NIMRRYLKQKLRNNDLKKQNKPAIPLPQILGLTASPGVGAAKKQSEAEKH
ILNICANLDAFTIKTVKENLGQLKHQIKEPCKKFVIADDTRENPFKEKLL
EIMASIQTYCQKSPMSDFGTQHYEQWAIQMEKKAAKDGNRKDRVCAEHLR
KYNEALQINDTIRMIDAYSHLETFYTDEKEKKFAVLNDSSLKLDETDEFL
MNLFFDNKKMLKKLAENPKYENEKLIKLRNTILEQFTRSEESSRGIIFTK
TRQSTYALSQWIMENAKFAEVGVKAHHLIGAGHSSEVKPMTQTEQKEVIS
KFRTGEINLLIATTVAEEGLDIKECNIVIRYGLVTNEIAMVQARGRARAD
ESTYVLVTSSGSGVTEREIVNDFREKMMYKAINRVQNMKPEEYAHKILEL
QVQSILEKKMKVKRSIAYNDNPSLITLLCKNCSMLVCSGENIHVIEKMHH
VNMTPEFKGLYIVRENKALQKDYQTNGEIICKCGQAWGTMMVHKGLDLPC
LKIRNFVVNFKNNSPKKQYKKWVELPIRFPDLDYSEYCL

3D structure

• PDB: 6gkm Cryo-EM Structures of MDA5-dsRNA Filaments at Different Stages of ATP Hydrolysis.
• Chain: A
• Resolution: 3.87 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 Q577 H578 H759 T767 T769 T811 R843 M926 H927 L947 N957 T970 K983 V1004	K145 E146 Q271 H272 H433 T441 T443 T485 R517 M598 H599 L619 N626 T639 K652 V673
BS02	rna	A	N365 V367 G393 K398 T414 Q416 K726 R728 G756 S761 T789 T790 V791 E924 H927 V973	N59 V61 G87 K92 T108 Q110 K400 R402 G430 S435 T463 T464 V465 E596 H599 V642
BS03	ZN	A	C907 C962 C964	C579 C631 C633
BS04	ATP	A	R310 G333 S334 G335 K336 T337 R338	R4 G27 S28 G29 K30 T31 R32

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