2GX9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   X-RAY STRUCUTRE OF INFLUENZA VIRUS NS1 EFFECTOR DOMAIN

Authors :   Z. A. Bornholdt, B. V. Prasad

Date :   08 May 06 (Deposition) - 30 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Ns1, Influenza, Effector Domain, Alpha-Helix Beta-Crescent, Transcription, Virus-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. A. Bornholdt, B. V. Prasad
X-Ray Structure Of Influenza Virus Ns1 Effector Domain.
Nat. Struct. Mol. Biol. V. 13 559 2006
PubMed-ID: 16715094 | Reference-DOI: 10.1038/NSMB1099

Molecule 1 - NS1 EFFECTOR DOMAIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	NS1 EFFECTOR DOMAIN
	Gene	:	SEGMENT 8 - NS1
	Organism Scientific	:	UNIDENTIFIED INFLUENZA VIRUS
	Organism Taxid	:	11309
	Strain	:	A/PUERTO RICO/8/34
	Synonym	:	NONSTRUCTURAL PROTEIN NS1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 15)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	SCN	3	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:123 , THR A:151 , GLU A:153 , HOH A:221 , HOH A:9957 , PRO B:164	BINDING SITE FOR RESIDUE SCN A 9901
2	AC2	SOFTWARE	LYS B:126 , ASN B:127 , GLU B:152 , GLU B:153	BINDING SITE FOR RESIDUE SCN B 9902
3	AC3	SOFTWARE	TRP A:102 , SER A:103 , ILE A:156 , HOH A:9918 , HOH A:9957	BINDING SITE FOR RESIDUE SCN A 9903

(no "SS Bond" information available for 2GX9)

Asymmetric/Biological Unit

No.	Residues
1	Trp A:203	-	Arg A:204

(no "SAP(SNP)/Variant" information available for 2GX9)

(no "PROSITE Motif" information available for 2GX9)

(no "Exon" information available for 2GX9)

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:127
 aligned with NS1_I34A1 | P03496 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:127
                                    88        98       108       118       128       138       148       158       168       178       188       198       
            NS1_I34A1    79 MTMASVPASRYLTDMTLEEMSRDWSMLIPKQKVAGPLCIRMDQAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNAVGVLIGGLEWNDNTVRVSETLQRFAWRS 205
               SCOP domains d2gx9a1 A:79-205 Non-structural protein NS1 C-terminal domain                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..hhhhhhh......eeeeee..eeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gx9 A  79 mTmASVPASRYLTDmTLEEmSRDWSmLIPKQKVAGPLCIRmDQAImDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNAVGVLIGGLEWNDNTVRVSETLQRFAWRS 205
                            | |     88    |   98     | 108       118|    | 128       138       148       158       168       178       188       198       
                            | |          93-MSE|     |            119-MSE|                                                                                 
                           79-MSE             98-MSE |                 124-MSE                                                                             
                             81-MSE                104-MSE

Chain A from PDB  Type:PROTEIN  Length:127
 aligned with Q6LD08_9INFA | Q6LD08 from UniProtKB/TrEMBL  Length:230

    Alignment length:127
                                    88        98       108       118       128       138       148       158       168       178       188       198       
         Q6LD08_9INFA    79 MTMASVPASRYLTDMTLEEMSRDWSMLIPKQKVAGPLCIRMDQAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNAVGVLIGGLEWNDNTVRVSETLQRFAWRS 205
               SCOP domains d2gx9a1 A:79-205 Non-structural protein NS1 C-terminal domain                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee..hhhhhhh......eeeeee..eeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gx9 A  79 mTmASVPASRYLTDmTLEEmSRDWSmLIPKQKVAGPLCIRmDQAImDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNAVGVLIGGLEWNDNTVRVSETLQRFAWRS 205
                            | |     88    |   98     | 108       118|    | 128       138       148       158       168       178       188       198       
                           79-MSE        93-MSE|     |            119-MSE|                                                                                 
                             81-MSE           98-MSE |                 124-MSE                                                                             
                                                   104-MSE

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with NS1_I34A1 | P03496 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:122
                                    95       105       115       125       135       145       155       165       175       185       195       205  
            NS1_I34A1    86 ASRYLTDMTLEEMSRDWSMLIPKQKVAGPLCIRMDQAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNAVGVLIGGLEWNDNTVRVSETLQRFAWRSSN 207
               SCOP domains d2gx9b_ B: Non-structural protein NS1 C-terminal domain                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhh......eeeeee..eeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gx9 B  86 ASRYLTDmTLEEmSRDWSmLIPKQKVAGPLCIRmDQAImDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNAVGVLIGGLEWNDNTVRVSETLQRFAWRSSN 207
                                   |95  |    105       115   |   125       135       145       155       165       175       185       195       205  
                                  93-MSE|     |            119-MSE|                                                                                   
                                       98-MSE |                 124-MSE                                                                               
                                            104-MSE

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with Q6LD08_9INFA | Q6LD08 from UniProtKB/TrEMBL  Length:230

    Alignment length:122
                                    95       105       115       125       135       145       155       165       175       185       195       205  
         Q6LD08_9INFA    86 ASRYLTDMTLEEMSRDWSMLIPKQKVAGPLCIRMDQAIMDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNAVGVLIGGLEWNDNTVRVSETLQRFAWRSSN 207
               SCOP domains d2gx9b_ B: Non-structural protein NS1 C-terminal domain                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..hhhhhhh......eeeeee..eeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gx9 B  86 ASRYLTDmTLEEmSRDWSmLIPKQKVAGPLCIRmDQAImDKNIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTAEDVKNAVGVLIGGLEWNDNTVRVSETLQRFAWRSSN 207
                                   |95  |    105       115   |   125       135       145       155       165       175       185       195       205  
                                  93-MSE|     |            119-MSE|                                                                                   
                                       98-MSE |                 124-MSE                                                                               
                                            104-MSE

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ns1 effector domain-like (19)

Superfamily: Ns1 effector domain-like (19)

Family: Ns1 effector domain-like (19)

Protein domain: Non-structural protein NS1 C-terminal domain (1)

Influenza A virus [TaxId: 11320] (1)

1a	d2gx9a1	A:79-205
1b	d2gx9b_	B:

(no "CATH Domain" information available for 2GX9)

(no "Pfam Domain" information available for 2GX9)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (Q6LD08_9INFA | Q6LD08)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039580	suppression by virus of host PKR activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (protein kinase regulated by RNA) activity. Activation of PKR involves dsRNA binding followed by autophosphorylation. Phosphorylated PKR can then phosphorylate downstream targets such as the translation initiation factor eIF2 to inhibit protein synthesis. Viruses encode a number of mechanisms to inhibit the host antiviral response via PKR, including direct interaction with PKR, promoting degradation of PKR or altering the subcellular location of PKR.
	GO:0039540	suppression by virus of host RIG-I activity	Any process in which a virus stops, prevents, or reduces the activity of RIG-1 (also known as DDX58). The cytoplasmic pattern recognition RIG-I recognizes viral RNA synthesized during active viral replication and signals to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
	GO:0039657	suppression by virus of host gene expression	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. 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 (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039524	suppression by virus of host mRNA processing	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of mRNA processing in the host cell. mRNA processing is the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0039502	suppression by virus of host type I interferon-mediated signaling pathway	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	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:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Chain A,B (NS1_I34A1 | P03496)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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).
biological process
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0075733	intracellular transport of virus	The directed movement of a virus, or part of a virus, within the host cell.
	GO:0046778	modification by virus of host mRNA processing	Any viral process that interferes with the processing of mRNA in the host cell.
	GO:0019054	modulation by virus of host process	The process in which a virus effects a change in the processes and activities of its host organism.
	GO:0039580	suppression by virus of host PKR activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host PKR (protein kinase regulated by RNA) activity. Activation of PKR involves dsRNA binding followed by autophosphorylation. Phosphorylated PKR can then phosphorylate downstream targets such as the translation initiation factor eIF2 to inhibit protein synthesis. Viruses encode a number of mechanisms to inhibit the host antiviral response via PKR, including direct interaction with PKR, promoting degradation of PKR or altering the subcellular location of PKR.
	GO:0039540	suppression by virus of host RIG-I activity	Any process in which a virus stops, prevents, or reduces the activity of RIG-1 (also known as DDX58). The cytoplasmic pattern recognition RIG-I recognizes viral RNA synthesized during active viral replication and signals to protect the host against viral infection, for example by inducing the expression of antiviral cytokines.
	GO:0039657	suppression by virus of host gene expression	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. 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 (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039524	suppression by virus of host mRNA processing	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of mRNA processing in the host cell. mRNA processing is the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
	GO:0039502	suppression by virus of host type I interferon-mediated signaling pathway	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	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.
	GO:0019083	viral transcription	The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
	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:0030430	host cell cytoplasm	The cytoplasm of a host cell.
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Trp A:203 - Arg A:204	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 2GX9)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 15)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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