3ZD7 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   SNAPSHOT 3 OF RIG-I SCANNING ON RNA DUPLEX

Authors :   D. Luo, A. M. Pyle

Date :   25 Nov 12 (Deposition) - 07 Aug 13 (Release) - 11 Sep 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,C,D
Biol. Unit 1: A,C,D  (1x)

Keywords :   Hydrolase-Rna Complex, Helicase, Innate Immunity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Kohlway, D. Luo, D. C. Rawling, S. C. Ding, A. M. Pyle
Defining The Functional Determinants For Rna Surveillance By Rig-I.
Embo Rep. V. 14 772 2013
PubMed-ID: 23897087 | Reference-DOI: 10.1038/EMBOR.2013.108

Molecule 1 - PROBABLE ATP-DEPENDENT RNA HELICASE DDX58
	Chains	:	A
	EC Number	:	3.6.4.13
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	DEAD BOX PROTEIN 58, RIG-I-LIKE RECEPTOR 1, RLR-1, RETINOIC ACID-INDUCIBLE GENE 1 PROTEIN, RIG-1, RETINOIC ACID-INDUCIBLE GENE I PROTEIN, RIG-I

Molecule 2 - RNA DUPLEX
	Chains	:	C, D
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2	3
Asymmetric Unit	:	A	C	D
Biological Unit 1 (1x)	:	A	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:810 , CYS A:813 , CYS A:864 , CYS A:869	BINDING SITE FOR RESIDUE ZN A 927
2	AC2	SOFTWARE	LYS A:270 , ASP A:372 , ADP A:1924	BINDING SITE FOR RESIDUE MG A1923
3	AC3	SOFTWARE	LEU A:237 , LYS A:242 , ARG A:244 , GLN A:247 , THR A:266 , GLY A:267 , CYS A:268 , GLY A:269 , LYS A:270 , THR A:271 , PHE A:272 , MG A:1923 , HOH A:2002	BINDING SITE FOR RESIDUE ADP A1924

Asymmetric Unit

No.	Residues
1	A:520	-	A:535

Asymmetric Unit

No.	Residues
1	Ser A:399	-	Gly A:400
2	Glu A:702	-	Gly A:703
3	Gly A:703	-	Ile A:704

Asymmetric Unit (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073667	C	268	F	DDX58_HUMAN	Disease (SGMRT2)	786204848	A	C	268	F
2	UniProt	VAR_073668	E	373	A	DDX58_HUMAN	Disease (SGMRT2)	786204847	A	E	373	A
3	UniProt	VAR_023748	D	580	E	DDX58_HUMAN	Polymorphism	17217280	A	D	580	E

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

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_073667	C	268	F	DDX58_HUMAN	Disease (SGMRT2)	786204848	A	C	268	F
2	UniProt	VAR_073668	E	373	A	DDX58_HUMAN	Disease (SGMRT2)	786204847	A	E	373	A
3	UniProt	VAR_023748	D	580	E	DDX58_HUMAN	Polymorphism	17217280	A	D	580	E

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RLR_CTR	PS51789	RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile.	DDX58_HUMAN	794-925	1	A:803-922

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RLR_CTR	PS51789	RIG-I-like receptor (RLR) C-terminal regulatory (CTR) domain profile.	DDX58_HUMAN	794-925	1	A:803-922

Asymmetric Unit (13, 13)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000379883	1a	ENSE00000928042	chr9:32526322-32526059	264	DDX58_HUMAN	1-36	36	0	-	-
1.2	ENST00000379883	2	ENSE00001788537	chr9:32500937-32500803	135	DDX58_HUMAN	36-81	46	0	-	-
1.3	ENST00000379883	3	ENSE00001679623	chr9:32493940-32493759	182	DDX58_HUMAN	81-141	61	0	-	-
1.4	ENST00000379883	4	ENSE00000695271	chr9:32492536-32492389	148	DDX58_HUMAN	142-191	50	0	-	-
1.5	ENST00000379883	5	ENSE00001797315	chr9:32491418-32491299	120	DDX58_HUMAN	191-231	41	0	-	-
1.6	ENST00000379883	6	ENSE00000695265	chr9:32489449-32489342	108	DDX58_HUMAN	231-267	37	1	A:236-267	32
1.7	ENST00000379883	7	ENSE00000695262	chr9:32488885-32488732	154	DDX58_HUMAN	267-318	52	1	A:267-318	52
1.8	ENST00000379883	8	ENSE00000695259	chr9:32488201-32487943	259	DDX58_HUMAN	318-404	87	1	A:318-404 (gaps)	87
1.9	ENST00000379883	9	ENSE00000695256	chr9:32487631-32487469	163	DDX58_HUMAN	405-459	55	1	A:405-459	55
1.10	ENST00000379883	10	ENSE00000695252	chr9:32485277-32485173	105	DDX58_HUMAN	459-494	36	1	A:459-494	36
1.11	ENST00000379883	11	ENSE00000695248	chr9:32481495-32481338	158	DDX58_HUMAN	494-546	53	1	A:494-546 (gaps)	53
1.12	ENST00000379883	12	ENSE00000928040	chr9:32480352-32480217	136	DDX58_HUMAN	547-592	46	1	A:547-592	46
1.13	ENST00000379883	13	ENSE00000982630	chr9:32477129-32476981	149	DDX58_HUMAN	592-641	50	1	A:592-641	50
1.14	ENST00000379883	14	ENSE00000982631	chr9:32473063-32472973	91	DDX58_HUMAN	642-672	31	1	A:642-662	21
1.15	ENST00000379883	15	ENSE00000982632	chr9:32467930-32467760	171	DDX58_HUMAN	672-729	58	1	A:692-720	29
1.16	ENST00000379883	16	ENSE00000982633	chr9:32466439-32466288	152	DDX58_HUMAN	729-779	51	1	A:733-779	47
1.17	ENST00000379883	17	ENSE00001091722	chr9:32459512-32459369	144	DDX58_HUMAN	780-827	48	1	A:780-827 (gaps)	48
1.18a	ENST00000379883	18a	ENSE00001247665	chr9:32457416-32455703	1714	DDX58_HUMAN	828-925	98	1	A:828-922 (gaps)	95

Asymmetric 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:623
 aligned with DDX58_HUMAN | O95786 from UniProtKB/Swiss-Prot  Length:925

    Alignment length:687
                                   245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835       845       855       865       875       885       895       905       915       
          DDX58_HUMAN   236 NLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQQKSVFSKYFERHGYRVTGISGATAENVPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQIQNREFGTQKYEQWIVTVQKACMVFQMPDKDEESRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILTGRGKTNQNTGMTLPAQKCILDAFKASGDHNILIATSVADEGIDIAQCNLVILYEYVGNVIKMIQTRGRGRARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDSQEKPKPVPDKENKKLLCRKCKALACYTADVRVIEECHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVEDIATGVQTLYSKWKDFHFEKIPFDPAE 922
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh......eeee.....--.hhhhhhhh..eeeehhhhhhhhhhh....hhhhh.eeeee.hhhh...hhhhhhhhhhhhhhhh.......eeeeee.........hhhhhhhhhhhhhhhh...eee....hhhhhh......eeeeee......hhhhhhhhhhhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhh...----------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee..hhhhhhhhhhhhhhhhhhh...eee..-----------------------------...eeee......hhhhh.eeeee.....------------....eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh---------....eeee.....eeee...eeee...eeee..hhhhhheeeeeeeeeee....eeeeeeee.......eeeeeeee..eeeeee....eeee.--...ee................... Sec.struct. author
                 SAPs(SNPs) --------------------------------F--------------------------------------------------------------------------------------------------------A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------E------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RLR_CTR  PDB: A:803-922 UniProt: 794-925                                                                                          PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:236-267        --------------------------------------------------Exon 1.8  PDB: A:318-404 (gaps) UniProt: 318-404                                       ------------------------------------------------------Exon 1.10  PDB: A:459-494           ----------------------------------------------------Exon 1.12  PDB: A:547-592 UniProt: 547-592    -------------------------------------------------Exon 1.14  PDB: A:642-662      --------------------------------------------------------Exon 1.16  PDB: A:733-779 UniProt: 729-779         Exon 1.17  PDB: A:780-827 (gaps)                Exon 1.18a  PDB: A:828-922 (gaps) UniProt: 828-925 [INCOMPLETE]                                 Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.7  PDB: A:267-318 UniProt: 267-318           --------------------------------------------------------------------------------------Exon 1.9  PDB: A:405-459 UniProt: 405-459              ----------------------------------Exon 1.11  PDB: A:494-546 (gaps) UniProt: 494-546    ---------------------------------------------Exon 1.13  PDB: A:592-641 UniProt: 592-641        ------------------------------Exon 1.15  PDB: A:692-720 UniProt: 672-729 [INCOMPLETE]   ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3zd7 A 236 NLYSPFKPRNYQLELALPAMKGKNTIICAPTGCGKTFVSLLICEHHLKKFPQGQKGKVVFFANQIPVYEQNKSVFSKYFERHGYRVTGISGATA--VPVEQIVENNDIIILTPQILVNNLKKGTIPSLSIFTLMIFDECHNTSKQHPYNMIMFNYLDQKLGGSSGPLPQVIGLTASVGVGDAKNTDEALDYICKLCASLDASVIATVKHNLEELEQVVYKPQKFFRKVESRISDKFKYIIAQLMRDTESLAKRICKDLENLSQSQNREFGTQKYEQWIVTVQKACM----------SRICKALFLYTSHLRKYNDALIISEHARMKDALDYLKDFFSNVRAAGFDEIEQDLTQRFEEKLQELESVSRDPSNENPKLEDLCFILQEEYHLNPETITILFVKTRALVDALKNWIEGNPKLSFLKPGILT-----------------------------NILILTSVADEGIDIAQCNLVILYEYVGN------------ARGSKCFLLTSNAGVIEKEQINMYKEKMMNDSILRLQTWDEAVFREKILHIQTHEKFIRDS---------KENKKLLCRKCKALACYTADVRVIEDCHYTVLGDAFKECFVSRPHPKPKQFSSFEKRAKIFCARQNCSHDWGIHVKYKTFEIPVIKIESFVVED--TGVQTLYSKWKDFHFEKIPFDPAE 922
                                   245       255       265       275       285       295       305       315       325   |  |335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515     |   -      |535       545       555       565       575       585       595       605       615       625       635       645       655      |  -         -         -      |695       705       715    |    -       735       745       755       765       775       785       | -       805       815       825       835       845       855       865       875       885       895|  |   905       915       
                                                                                                                       329  |                                                                                                                                                                                          521        532                                                                                                                               662                           692                         720          733                                                         793       803                                                                                          896  |                       
                                                                                                                          332                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    899

Chain C from PDB  Type:RNA  Length:10
                                          
                 3zd7 C   1 GCGCGCGCGC  10
                                    10

Chain D from PDB  Type:RNA  Length:10
                                          
                 3zd7 D   1 GCGCGCGCGC  10
                                    10

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 3ZD7)

(no "CATH Domain" information available for 3ZD7)

(no "Pfam Domain" information available for 3ZD7)

Asymmetric Unit(hide GO term definitions)

Chain A (DDX58_HUMAN | O95786)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	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:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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: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:0039529	RIG-I signaling pathway	Any series of molecular signals generated as a consequence of the cytoplasmic pattern recognition receptor (PRR) RIG-1 (also known as DDX58) binding to viral RNA. RIG-I 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:0002230	positive regulation of defense response to virus by host	Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0032725	positive regulation of granulocyte macrophage colony-stimulating factor production	Any process that activates or increases the frequency, rate, or extent of granulocyte macrophage colony-stimulating factor production.
	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:0032755	positive regulation of interleukin-6 production	Any process that activates or increases the frequency, rate, or extent of interleukin-6 production.
	GO:0032757	positive regulation of interleukin-8 production	Any process that activates or increases the frequency, rate, or extent of interleukin-8 production.
	GO:0051091	positive regulation of sequence-specific DNA binding transcription factor activity	Any process that activates or increases the frequency, rate or extent of activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0042993	positive regulation of transcription factor import into nucleus	Any process that activates or increases the frequency, rate or extent of the movement of a transcription factor from the cytoplasm to the nucleus.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0030334	regulation of cell migration	Any process that modulates the frequency, rate or extent of cell migration.
	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:0043330	response to exogenous dsRNA	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 an exogenous double-stranded RNA stimulus.
	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:0015629	actin cytoskeleton	The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
	GO:0005923	bicellular tight junction	An occluding cell-cell junction that is composed of a branching network of sealing strands that completely encircles the apical end of each cell in an epithelial sheet; the outer leaflets of the two interacting plasma membranes are seen to be tightly apposed where sealing strands are present. Each sealing strand is composed of a long row of transmembrane adhesion proteins embedded in each of the two interacting plasma membranes.
	GO:0030054	cell junction	A cellular component that forms a specialized region of connection between two or more cells or between a cell and the extracellular matrix. At a cell junction, anchoring proteins extend through the plasma membrane to link cytoskeletal proteins in one cell to cytoskeletal proteins in neighboring cells or to proteins in the extracellular matrix.
	GO:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0032587	ruffle membrane	The portion of the plasma membrane surrounding a ruffle.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:702 - Gly A:703	[ RasMol ]
		Gly A:703 - Ile A:704	[ RasMol ]
		Ser A:399 - Gly A:400	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	3zd7
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Access by UniProt ID/Accession number
	DDX58_HUMAN \| O95786
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	3.6.4.13
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	616298
		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
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	DDX58_HUMAN \| O95786
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

3zd6	SNAPSHOT 1 OF RIG-I SCANNING ON RNA DUPLEX

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (1, 1)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 3)

PROSITE Motifs (1, 1)

Exons (13, 13)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (46, 46)

Visualization

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Still Images

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Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File