3B6E - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN DECH-BOX RNA HELICASE MDA5 (MELANOMA DIFFERENTIATION-ASSOCIATED PROTEIN 5), DECH-DOMAIN

Authors :   T. Karlberg, M. Welin, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Col L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Ham I. Johansson, A. Kallas, T. Kotenyova, L. Lehtio, M. Moche, M. E. Nilss P. Nordlund, T. Nyman, C. Persson, J. Sagemark, L. Svensson, A. G. Thor L. Tresaugues, S. Van Den Berg, J. Weigelt, L. Holmberg-Schiavone, Structural Genomics Consortium (Sgc)

Date :   29 Oct 07 (Deposition) - 13 Nov 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Dech, Dexd/H Rna-Binding Helicase, Innate Immunity, Ifih1, Structural Genomics, Structural Genomics Consortium, Sgc, Antiviral Defense, Atp-Binding, Diabetes Mellitus, Host-Virus Interaction, Hydrolase, Immune Response, Nucleotide-Binding, Nucleus, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Karlberg, M. Welin, C. H. Arrowsmith, H. Berglund, R. D. Busam, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Johansson, A. Kallas, T. Kotenyova, L. Lehtio, M. Moche, M. E. Nilsson, P. Nordlund, T. Nyman, C. Persson, J. Sagemark, L. Svensson, A. G. Thorsell, L. Tresaugues, S. Van Den Berg, J. Weigelt, L. Holmberg-Schiavone
Human Dech-Box Rna Helicase Mda5 (Melanoma Differentiation-Associated Protein 5), Dech-Domain.
To Be Published
PubMed: search

Molecule 1 - INTERFERON-INDUCED HELICASE C DOMAIN-CONTAINING PROTEIN 1
	Chains	:	A
	EC Number	:	3.6.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PNIC-BSA4
	Expression System Strain	:	BL21(DE3) GOLD PRARE2
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	DECH DOMAIN: RESIDUES 277-490
	Gene	:	IFIH1, MDA5, RH116
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	INTERFERON-INDUCED WITH HELICASE C DOMAIN PROTEIN 1, HELICASE WITH 2 CARD DOMAINS, HELICARD, MELANOMA DIFFERENTIATION- ASSOCIATED PROTEIN 5, MDA-5, RNA HELICASE-DEAD BOX PROTEIN 116, MURABUTIDE DOWN-REGULATED PROTEIN

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NA	1	Ligand/Ion	SODIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:83 , ARG A:309 , GLN A:312 , PRO A:330 , THR A:331	BINDING SITE FOR RESIDUE NA A 600

(no "SS Bond" information available for 3B6E)

Asymmetric/Biological Unit

No.	Residues
1	Ala A:489	-	Ser A:490

Asymmetric/Biological Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_071375	R	337	G	IFIH1_HUMAN	Disease (AGS7)	587777447	A	R	337	G
2	UniProt	VAR_071376	L	372	F	IFIH1_HUMAN	Disease (AGS7)	587777576	A	L	372	F
3	UniProt	VAR_031226	H	460	R	IFIH1_HUMAN	Polymorphism	10930046	A	H	460	R

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 3B6E)

Asymmetric/Biological Unit (4, 4)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000263642	1a	ENSE00001858759	chr2:163175213-163174365	849	IFIH1_HUMAN	1-151	151	0	-	-
1.2a	ENST00000263642	2a	ENSE00000840792	chr2:163167443-163167275	169	IFIH1_HUMAN	152-208	57	0	-	-
1.3b	ENST00000263642	3b	ENSE00000840791	chr2:163163365-163163219	147	IFIH1_HUMAN	208-257	50	0	-	-
1.4	ENST00000263642	4	ENSE00000840790	chr2:163150178-163150074	105	IFIH1_HUMAN	257-292	36	1	A:292-292	1
1.5	ENST00000263642	5	ENSE00000840789	chr2:163144865-163144645	221	IFIH1_HUMAN	292-365	74	1	A:292-365	74
1.6	ENST00000263642	6	ENSE00000840788	chr2:163139086-163138876	211	IFIH1_HUMAN	366-436	71	1	A:366-436 (gaps)	71
1.7	ENST00000263642	7	ENSE00001073453	chr2:163138055-163137838	218	IFIH1_HUMAN	436-508	73	1	A:436-490 (gaps)	55
1.8	ENST00000263642	8	ENSE00001073457	chr2:163136622-163136506	117	IFIH1_HUMAN	509-547	39	0	-	-
1.9	ENST00000263642	9	ENSE00001073451	chr2:163134838-163134715	124	IFIH1_HUMAN	548-589	42	0	-	-
1.10	ENST00000263642	10	ENSE00001073449	chr2:163134203-163133925	279	IFIH1_HUMAN	589-682	94	0	-	-
1.11	ENST00000263642	11	ENSE00001073452	chr2:163133456-163133197	260	IFIH1_HUMAN	682-768	87	0	-	-
1.12	ENST00000263642	12	ENSE00001073458	chr2:163130454-163130305	150	IFIH1_HUMAN	769-818	50	0	-	-
1.13	ENST00000263642	13	ENSE00001073450	chr2:163128897-163128736	162	IFIH1_HUMAN	819-872	54	0	-	-
1.14	ENST00000263642	14	ENSE00001073448	chr2:163124787-163124597	191	IFIH1_HUMAN	873-936	64	0	-	-
1.15	ENST00000263642	15	ENSE00001073454	chr2:163124079-163123989	91	IFIH1_HUMAN	936-966	31	0	-	-
1.16	ENST00000263642	16	ENSE00001073456	chr2:163123889-163123589	301	IFIH1_HUMAN	967-1025	59	0	-	-

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:182
 aligned with IFIH1_HUMAN | Q9BYX4 from UniProtKB/Swiss-Prot  Length:1025

    Alignment length:199
                                   301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481         
          IFIH1_HUMAN   292 DEENVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSGDTQLKISFPEVVKSCDIIISTAQILENSLLNLENGEDAGVQLSDFSLIIIDECHHTNKEAVYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS 490
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b6eA00 A:292-490 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh........hhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhhhhhh....eee...---...hhhhhhhhh.eeeeehhhhhhhhhh-------..hhhhh.eeee...-------hhhhhhhhhhhhhhhhhhhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------G----------------------------------F---------------------------------------------------------------------------------------R------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1-------------------------------------------------------------------------Exon 1.6  PDB: A:366-436 (gaps) UniProt: 366-436                       ------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) Exon 1.5  PDB: A:292-365 UniProt: 292-365                                 ----------------------------------------------------------------------Exon 1.7  PDB: A:436-490 (gaps) UniProt: 436-508        Transcript 1 (2)
                 3b6e A 292 DEENVAARASPEPELQLRPYQMEVAQPALEGKNIIICLPTGSGKTRVAVYIAKDHLDKKKKASEPGKVIVLVNKVLLVEQLFRKEFQPFLKKWYRVIGLSG---LKISFPEVVKSCDIIISTAQILENSLLN-------GVQLSDFSLIIIDEC-------VYNNIMRHYLMQKLKNNRLKKENKPVIPLPQILGLTAS 490
                                   301       311       321       331       341       351       361       371       381       391|   |  401       411       421 |     431       441   |     - |     461       471       481         
                                                                                                                              392 396                        423     431           445     453

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3B6E)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Human (Homo sapiens) (413)

3b6eA00

A:292-490

(no "Pfam Domain" information available for 3B6E)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (IFIH1_HUMAN | Q9BYX4)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003725	double-stranded RNA binding	Interacting selectively and non-covalently with double-stranded RNA.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0016817	hydrolase activity, acting on acid anhydrides	Catalysis of the hydrolysis of any acid anhydride.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0043021	ribonucleoprotein complex binding	Interacting selectively and non-covalently with any complex of RNA and protein.
	GO:0003727	single-stranded RNA binding	Interacting selectively and non-covalently with single-stranded RNA.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0039530	MDA-5 signaling pathway	Any series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) MDA-5 (also known as IFIH1) binding to viral RNA. MDA-5 detects RNA synthesized during active viral replication and triggers a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
	GO:0039528	cytoplasmic pattern recognition receptor signaling pathway in response to virus	Any series of molecular signals generated as a consequence of a virus or viral RNA binding to a pattern recognition receptor (PRR) located in the cytoplasm. Cytosolic PRRs such as RIG-I (DDX58) and MDA-5 (IFIH1) detect RNA synthesized during active viral replication and trigger a signaling pathway to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
	GO:0051607	defense response to virus	Reactions triggered in response to the presence of a virus that act to protect the cell or organism.
	GO:0009597	detection of virus	The series of events in which a stimulus from a virus is received and converted into a molecular signal.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0032480	negative regulation of type I interferon production	Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0032727	positive regulation of interferon-alpha production	Any process that activates or increases the frequency, rate, or extent of interferon-alpha production.
	GO:0032728	positive regulation of interferon-beta production	Any process that activates or increases the frequency, rate, or extent of interferon-beta production.
	GO:0016925	protein sumoylation	The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
	GO:0034344	regulation of type III interferon production	Any process that modulates the frequency, rate, or extent of type III interferon production. Interferon lambda is the only member of the type III interferon found so far.
	GO:0009615	response to virus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	IFIH1_HUMAN \| Q9BYX4	:	2rqb 3ga3 4gl2

(no "Related Entries Specified in the PDB File" available for 3B6E)

Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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