4DS0 - JenaLib

Title :   CELL ATTACHMENT PROTEIN VP8* OF A HUMAN ROTAVIRUS SPECIFICALLY INTERACTS WITH A-TYPE HISTO-BLOOD GROUP ANTIGEN

Authors :   L. Hu, S. E. Crawford, R. Czako, N. W. Cortes-Penfield, D. F. Smith, J. Le M. K. Estes, B. V. V. Prasad

Date :   17 Feb 12 (Deposition) - 11 Apr 12 (Release) - 23 May 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.56

Chains :   Asym./Biol. Unit : A

Keywords :   Otavirus, Viral Protein, Cell Attachment Factor, Histo Blood Group Antigen, Galectin-Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Hu, S. E. Crawford, R. Czako, N. W. Cortes-Penfield, D. F. Smith, J. Le Pendu, M. K. Estes, B. V. Prasad
Cell Attachment Protein Vp8* Of A Human Rotavirus Specifically Interacts With A-Type Histo-Blood Group Antigen.
Nature V. 485 256 2012
PubMed-ID: 22504179 | Reference-DOI: 10.1038/NATURE10996

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:101 , TYR A:189 , LEU A:190 , THR A:191 , GAL A:302 , FUC A:303 , HOH A:651	BINDING SITE FOR RESIDUE A2G A 301
2	AC2	SOFTWARE	SER A:187 , TYR A:188 , TYR A:189 , A2G A:301 , FUC A:303 , NAG A:304 , HOH A:463 , HOH A:633 , HOH A:648	BINDING SITE FOR RESIDUE GAL A 302
3	AC3	SOFTWARE	ASP A:202 , A2G A:301 , GAL A:302 , NAG A:304 , HOH A:481	BINDING SITE FOR RESIDUE FUC A 303
4	AC4	SOFTWARE	PRO A:71 , THR A:87 , GLN A:88 , ASP A:202 , GAL A:302 , FUC A:303 , HOH A:463 , HOH A:566 , HOH A:633 , HOH A:639 , HOH A:641 , HOH A:648	BINDING SITE FOR RESIDUE NAG A 304

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:163
 aligned with Q86169_9REOV | Q86169 from UniProtKB/TrEMBL  Length:776

    Alignment length:163
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
         Q86169_9REOV    62 QPTLDGPYQPTTFNLPIDYWMLIAPTQIGRVAEGTNTTDRWFACVLVEPNVQNTQREYVLDGQTVQLQVSNNSSTLWKFILFIKLEKNGAYSQYSTLSTSNKLCAWMKREGRVYWYAGTTPNASESYYLTINNDNSNVSCDAEFYLIPRSQTELCTQYINNGL 224
               SCOP domains d4ds0a_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...ee.....eeeee.....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeeee......eeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ds0 A  62 GSTLDGPYQPTTFNLPIDYWMLIAPTQIGRVAEGTNTTDRWFACVLVEPNVQNTQREYVLDGQTVQLQVSNNSSTLWKFILFIKLEKNGAYSQYSTLSTSNKLCAWMKREGRVYWYAGTTPNASESYYLTINNDNSNVSCDAEFYLIPRSQTELCTQYINNGL 224
                                    71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

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 (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q86169_9REOV | Q86169)

biological process
	GO:0039665	permeabilization of host organelle membrane involved in viral entry into host cell	Induction of organellar membrane permeabilization triggered by an interaction between the host membrane and a membrane-penetration protein associated with a viral capsid. Results in release of the virus contents from an organelle into the host cell cytoplasm.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	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:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044165	host cell endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0044168	host cell rough endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the host cell cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The host rough ER has ribosomes adhering to the outer surface.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0039624	viral outer capsid	The outer layer of a double or triple concentric icosahedral capsid. Outer capsids are part of reoviridae and cystoviridae virions.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Visualization

Interactive Views

Asymmetric/Biological 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
		A2G	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		FUC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:67 - Pro A:68	[ RasMol ]
		Thr A:181 - Pro A:182	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4ds0
		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
	Q86169_9REOV \| Q86169
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q86169_9REOV \| Q86169
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description