3P31 - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE NS1 EFFECTOR DOMAIN FROM INFLUENZA A/VIETNAM/1203/2004 (H5N1) VIRUS

Authors :   S. Chen, Y. B. Xiao, R. Ponnusamy, R. Hilgenfeld

Date :   04 Oct 10 (Deposition) - 05 Oct 11 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A  (2x)
Biol. Unit 4: C  (2x)

Keywords :   Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Chen, Y. B. Xiao, R. Ponnusamy, R. Hilgenfeld
X-Ray Structures Of The Ns1 Effector Domain From Highly Pathogenic Influenza A/Vietnam/1203/2004 (H5N1) Virus
To Be Published
PubMed: search

Molecule 1 - NONSTRUCTURAL PROTEIN 1
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL EFFECTOR DOMAIN, UNP RESIDUES 73-215
	Gene	:	NS1
	Organism Scientific	:	INFLUENZA A VIRUS
	Organism Taxid	:	680789
	Strain	:	A/ENVIRONMENT/VIET NAM/1203/2004 (H5N1)

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (2x)	:	A
Biological Unit 4 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	SCN	8	Ligand/Ion	THIOCYANATE ION

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	SCN	6	Ligand/Ion	THIOCYANATE ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	SCN	2	Ligand/Ion	THIOCYANATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	SCN	2	Ligand/Ion	THIOCYANATE ION

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	SCN	2	Ligand/Ion	THIOCYANATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:107 , ASN A:171	BINDING SITE FOR RESIDUE SCN A 1
2	AC2	SOFTWARE	LYS B:126	BINDING SITE FOR RESIDUE SCN B 5
3	AC3	SOFTWARE	TRP B:97 , MET B:99 , LYS B:113	BINDING SITE FOR RESIDUE SCN B 6
4	AC4	SOFTWARE	SCN B:8 , MET B:93 , SER B:94 , ASP B:96 , ARG B:143	BINDING SITE FOR RESIDUE SCN B 7
5	AC5	SOFTWARE	SCN B:7	BINDING SITE FOR RESIDUE SCN B 8
6	AC6	SOFTWARE	HOH D:61 , TRP D:97 , LYS D:113	BINDING SITE FOR RESIDUE SCN D 3

(no "SS Bond" information available for 3P31)

Asymmetric Unit

No.	Residues
1	Leu A:161	-	Pro A:162
2	Pro B:162	-	Gly B:163

(no "SAP(SNP)/Variant" information available for 3P31)

(no "PROSITE Motif" information available for 3P31)

(no "Exon" information available for 3P31)

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 D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:120
                                    89        99       109       119       129       139       149       159       169       179       189       199
         D1LP63_9INFA    80 PASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWR 199
               SCOP domains d3p31a_ A: automated matches                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..hhhhhhh..........ee..eeeee.......eeeeeeeeeee..eeeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhh...eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p31 A  80 PASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWR 199
                                    89        99       109       119       129       139       149       159       169       179       189       199

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:121
                                    89        99       109       119       129       139       149       159       169       179       189       199 
         D1LP63_9INFA    80 PASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRN 200
               SCOP domains d3p31b_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhh......eeeee...eeeeee......eeeeeeeeeee..eeeeeeeeeeee....eeeeeee.......hhhhhhhhhhhhhhhhhhhh.eeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p31 B  80 PASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRN 200
                                    89        99       109       119       129       139       149       159       169       179       189       199

Chain C from PDB  Type:PROTEIN  Length:122
 aligned with D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:122
                                    90       100       110       120       130       140       150       160       170       180       190       200  
         D1LP63_9INFA    81 ASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRNSD 202
               SCOP domains d3p31c_ C: automated matches                                                                                               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
                 3p31 C  81 ASRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRNSD 202
                                    90       100       110       120       130       140       150       160       170       180       190       200

Chain D from PDB  Type:PROTEIN  Length:121
 aligned with D1LP63_9INFA | D1LP63 from UniProtKB/TrEMBL  Length:215

    Alignment length:121
                                    91       101       111       121       131       141       151       161       171       181       191       201 
         D1LP63_9INFA    82 SRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRNSD 202
               SCOP domains d3p31d_ D: automated matches                                                                                              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
                 3p31 D  82 SRYLTDMTLEEMSRDWFMLMPKQKVAGSLCIKMDQAIMDKTIILKANFSVIFDRLETLILLRAFTEEGAIVGEISPLPSLPGHTGEDVKNAIGVLIGGLEWNDNTVRVTETIQRFAWRNSD 202
                                    91       101       111       121       131       141       151       161       171       181       191       201

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 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: automated matches (18)

Influenza A virus [TaxId: 680789] (3)

1a	d3p31a_	A:
1b	d3p31b_	B:
1c	d3p31c_	C:
1d	d3p31d_	D:

(no "CATH Domain" information available for 3P31)

(no "Pfam Domain" information available for 3P31)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (D1LP63_9INFA | D1LP63)

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.

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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