4A2X - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF DUCK RIG-I C-TERMINAL DOMAIN (CTD) WITH 14-MER DSRNA

Authors :   E. Kowalinski, T. Lunardi, A. A. Mccarthy, S. Cusack

Date :   29 Sep 11 (Deposition) - 19 Oct 11 (Release) - 26 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.00

Chains :   Asym. Unit : A,B,C,D,L,M,N,O
Biol. Unit 1: A,B,L,M  (1x)
Biol. Unit 2: C,D,N,O  (1x)

Keywords :   Rna Binding Protein-Rna Complex, Superfamily 2 Rna Helicase, Atp And Dsrna Binding, Antiviral Signalling Pathway (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Kowalinski, T. Lunardi, A. A. Mccarthy, J. Louber, J. Brunel, B. Grigorov, D. Gerlier, S. Cusack
Structural Basis For The Activation Of Innate Immune Patter Recognition Receptor Rig-I By Viral Rna.
Cell(Cambridge, Mass. ) V. 147 423 2011
PubMed-ID: 22000019 | Reference-DOI: 10.1016/J.CELL.2011.09.039

Molecule 1 - RETINOIC ACID INDUCIBLE PROTEIN I
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	STAR
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN, RESIDUES 806-933
	Organism Common	:	MALLARD DUCK
	Organism Scientific	:	ANAS PLATYRHYNCHOS
	Organism Taxid	:	8839
	Synonym	:	RIG-I

*Molecule 2 - 5'-R(GPGPGPAPGPAPAPCPAPAPCPGPCPGP)-3'*
	Chains	:	L, N
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synonym	:	14-MER RNA
	Synthetic	:	YES

*Molecule 3 - 5'-R(CPGPCPGPUPUPGPUPUPCPUPCPCPCP)-3'*
	Chains	:	M, O
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	L	M	N	O
Biological Unit 1 (1x)	:	A	B			L	M
Biological Unit 2 (1x)	:			C	D			N	O

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:812 , CYS A:815 , CYS A:866 , CYS A:871	BINDING SITE FOR RESIDUE ZN A1000
2	AC2	SOFTWARE	CYS B:812 , CYS B:815 , CYS B:866 , CYS B:871	BINDING SITE FOR RESIDUE ZN B1000
3	AC3	SOFTWARE	CYS C:812 , CYS C:815 , CYS C:866 , CYS C:871	BINDING SITE FOR RESIDUE ZN C1000
4	AC4	SOFTWARE	CYS D:812 , CYS D:815 , CYS D:866 , CYS D:871	BINDING SITE FOR RESIDUE ZN D1000

(no "SS Bond" information available for 4A2X)

(no "Cis Peptide Bond" information available for 4A2X)

(no "SAP(SNP)/Variant" information available for 4A2X)

(no "PROSITE Motif" information available for 4A2X)

(no "Exon" information available for 4A2X)

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:120
 aligned with D3TI84_ANAPL | D3TI84 from UniProtKB/TrEMBL  Length:933

    Alignment length:125
                                   816       826       836       846       856       866       876       886       896       906       916       926     
         D3TI84_ANAPL   807 QKNLLCGKCKAYACSTDDIRIIKDSHHIVLGEAFKERYTTKPHKKPMQFDGFEKKSKMYCRNNNCQHDWGITVKYLTFDNLPVIKIKSFVMESTATGTQMDFQKWKSINSSLKNFDVEEMSNLYP 931
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeee...eeee...eeee.hhhhhh.eeeee.....ee..eeeeeeeee.......eeeeeeee..eeeeeee....eee..-----..hhhhhhhhh......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a2x A 807 QKNLLCGKCKAYACSTDDIRIIKDSHHIVLGEAFKERYTTKPHKKPMQFDGFEKKSKMYCRNNNCQHDWGITVKYLTFDNLPVIKIKSFVMES-----QMDFQKWKSINSSLKNFDVEEMSNLYP 931
                                   816       826       836       846       856       866       876       886       896  |    906       916       926     
                                                                                                                      899   905

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with D3TI84_ANAPL | D3TI84 from UniProtKB/TrEMBL  Length:933

    Alignment length:125
                                   816       826       836       846       856       866       876       886       896       906       916       926     
         D3TI84_ANAPL   807 QKNLLCGKCKAYACSTDDIRIIKDSHHIVLGEAFKERYTTKPHKKPMQFDGFEKKSKMYCRNNNCQHDWGITVKYLTFDNLPVIKIKSFVMESTATGTQMDFQKWKSINSSLKNFDVEEMSNLYP 931
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeee...eeee...eeee.hhhhhh.eeeee.....ee..eeeeeeeee.......eeeeeeee..eeeeeee....eee..-----..hhhhhhhhh......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a2x B 807 QKNLLCGKCKAYACSTDDIRIIKDSHHIVLGEAFKERYTTKPHKKPMQFDGFEKKSKMYCRNNNCQHDWGITVKYLTFDNLPVIKIKSFVMES-----QMDFQKWKSINSSLKNFDVEEMSNLYP 931
                                   816       826       836       846       856       866       876       886       896  |    906       916       926     
                                                                                                                      899   905

Chain C from PDB  Type:PROTEIN  Length:120
 aligned with D3TI84_ANAPL | D3TI84 from UniProtKB/TrEMBL  Length:933

    Alignment length:125
                                   816       826       836       846       856       866       876       886       896       906       916       926     
         D3TI84_ANAPL   807 QKNLLCGKCKAYACSTDDIRIIKDSHHIVLGEAFKERYTTKPHKKPMQFDGFEKKSKMYCRNNNCQHDWGITVKYLTFDNLPVIKIKSFVMESTATGTQMDFQKWKSINSSLKNFDVEEMSNLYP 931
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeee...eeee...eeee.hhhhhh.eeeee.....ee..eeeeeeeee.......eeeeeeee..eeeeeee....eee..-----..hhhhhhhhh......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a2x C 807 QKNLLCGKCKAYACSTDDIRIIKDSHHIVLGEAFKERYTTKPHKKPMQFDGFEKKSKMYCRNNNCQHDWGITVKYLTFDNLPVIKIKSFVMES-----QMDFQKWKSINSSLKNFDVEEMSNLYP 931
                                   816       826       836       846       856       866       876       886       896  |    906       916       926     
                                                                                                                      899   905

Chain D from PDB  Type:PROTEIN  Length:120
 aligned with D3TI84_ANAPL | D3TI84 from UniProtKB/TrEMBL  Length:933

    Alignment length:125
                                   816       826       836       846       856       866       876       886       896       906       916       926     
         D3TI84_ANAPL   807 QKNLLCGKCKAYACSTDDIRIIKDSHHIVLGEAFKERYTTKPHKKPMQFDGFEKKSKMYCRNNNCQHDWGITVKYLTFDNLPVIKIKSFVMESTATGTQMDFQKWKSINSSLKNFDVEEMSNLYP 931
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.....eeee...eeee...eeee.hhhhhh.eeeee.....ee..eeeeeeeee.......eeeeeeee..eeeeeee....eee..-----..hhhhhhhhh......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4a2x D 807 QKNLLCGKCKAYACSTDDIRIIKDSHHIVLGEAFKERYTTKPHKKPMQFDGFEKKSKMYCRNNNCQHDWGITVKYLTFDNLPVIKIKSFVMES-----QMDFQKWKSINSSLKNFDVEEMSNLYP 931
                                   816       826       836       846       856       866       876       886       896  |    906       916       926     
                                                                                                                      899   905

Chain L from PDB  Type:RNA  Length:14
                                              
                 4a2x L   1 GGGAGAACAACGCG  14
                                    10

Chain M from PDB  Type:RNA  Length:14
                                              
                 4a2x M   1 CGCGUUGUUCUCCC  14
                                    10

Chain N from PDB  Type:RNA  Length:14
                                              
                 4a2x N   1 GGGAGAACAACGCG  14
                                    10

Chain O from PDB  Type:RNA  Length:14
                                              
                 4a2x O   1 CGCGUUGUUCUCCC  14
                                    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 4A2X)

(no "CATH Domain" information available for 4A2X)

(no "Pfam Domain" information available for 4A2X)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (D3TI84_ANAPL | D3TI84)

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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4a2x)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
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	4a2x
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	D3TI84_ANAPL \| D3TI84	:	4a2p 4a2q 4a2v 4a2w 4a36

4a2p	STRUCTURE OF DUCK RIG-I HELICASE DOMAIN
4a2q	STRUCTURE OF DUCK RIG-I TANDEM CARDS AND HELICASE DOMAIN
4a2v	STRUCTURE OF DUCK RIG-I C-TERMINAL DOMAIN (CTD)
4a2w	STRUCTURE OF FULL-LENGTH DUCK RIG-I
4a36	STRUCTURE OF DUCK RIG-I HELICASE DOMAIN BOUND TO 19 -MER DSRNA AND ATP TRANSITION STATE ANALOGUE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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Gene Ontology (7, 7)

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