2VVX - JenaLib

Title :   STRUCTURE OF VACCINIA VIRUS PROTEIN A52

Authors :   S. C. Graham, M. W. Bahar, S. Cooray, R. A. -J. Chen, D. M. Whalen, N. G. A. Abrescia, D. Alderton, R. J. Owens, D. I. Stuart, G. L. Smith, J. M. Grimes

Date :   12 Jun 08 (Deposition) - 26 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.75

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

Keywords :   Irak2, Traf6, Bcl-2 Family, Vaccinia Virus, Immunomodulator, Nf-Kb Activation, Viral Protein, Host-Virus Interaction (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. C. Graham, M. W. Bahar, S. Cooray, R. A. -J. Chen, D. M. Whalen, N. G. A. Abrescia, D. Alderton, R. J. Owens, D. I. Stuart, G. L. Smith, J. M. Grimes
Vaccinia Virus Proteins A52 And B14 Share A Bcl-2- Like Fold But Have Evolved To Inhibit Nf-Kappab Rather Than Apoptosis
Plos Pathog. V. 4 E128 2008
PubMed-ID: 18704168 | Reference-DOI: 10.1371/JOURNAL.PPAT.1000128

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:153
 aligned with A52_VACCW | Q01220 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:153
                                                                                                                                                                                190  
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189|  
            A52_VACCW    40 IKPDYLEYDDLLDRDEMFTILEEYFMYRGLLGLRIKYGRLFNEIKKFDNDAEEQFGTIEELKQKLRLNSEEGADNFIDYIKVQKQDIVKLTVYDCISMIGLCACVVDVWRNEKLFSRWKYCLRAIKLFINDHMLDKIKSILQNRLVYVEMS--   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvx A  40 IKPDYLEYDDLLDRDEMFTILEEYFMYRGLLGLRIKYGRLFNEIKKFDNDAEEQFGTIEELKQKLRLNSEEGADNFIDYIKVQKQDIVKLTVYDCISMIGLCACVVDVWRNEKLFSRWKYCLRAIKLFINDHMLDKIKSILQNRLVYVEMSKH 192
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with A52_VACCW | Q01220 from UniProtKB/Swiss-Prot  Length:190

    Alignment length:151
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189 
            A52_VACCW    40 IKPDYLEYDDLLDRDEMFTILEEYFMYRGLLGLRIKYGRLFNEIKKFDNDAEEQFGTIEELKQKLRLNSEEGADNFIDYIKVQKQDIVKLTVYDCISMIGLCACVVDVWRNEKLFSRWKYCLRAIKLFINDHMLDKIKSILQNRLVYVEMS 190
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh..hhhhhhhh......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vvx B  40 IKPDYLEYDDLLDRDEMFTILEEYFMYRGLLGLRIKYGRLFNEIKKFDNDAEEQFGTIEELKQKLRLNSEEGADNFIDYIKVQKQDIVKLTVYDCISMIGLCACVVDVWRNEKLFSRWKYCLRAIKLFINDHMLDKIKSILQNRLVYVEMS 190
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Asymmetric Unit(hide GO term definitions)

Chain A,B (A52_VACCW | Q01220)

molecular function
	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:0039644	suppression by virus of host NF-kappaB transcription factor activity	Any process in which a virus stops, prevents, or reduces the activity of host NF-kappaB activity.
	GO:0039547	suppression by virus of host TRAF activity	Any process in which a virus stops, prevents, or reduces the activity of a host TRAF (tumor necrosis factor receptor-associated factor) protein. TRAFs are intracellular signal transducers that lie downstream of receptors including RIG-I, MDA-5 and Toll-like receptors (TLR) and transfer the signal to other intracellular signaling components.
	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: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.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2vvx)

	Sites
(no "Sites" information available for 2vvx)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vvx)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	2vvx
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	A52_VACCW \| Q01220
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Description