3TB0 - JenaLib

Title :   CRYSTAL STRUCTURE OF RHESUS ROTAVIRUS VP8* IN COMPLEX WITH N-GLYCOLYLNEURAMINIC ACID

Authors :   X. Yu, H. Blanchard

Date :   04 Aug 11 (Deposition) - 17 Oct 12 (Release) - 05 Dec 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Beta Sandwich, Lectin, Sugar Binding Protein, Viral Protein, Neu5Gc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Yu, V. T. Dang, F. E. Fleming, M. Von Itzstein, B. S. Coulson, H. Blanchard
Structural Basis Of Rotavirus Strain Preference Toward N-Acetyl- Or N-Glycolylneuraminic Acid-Containing Receptors
J. Virol. V. 86 13456 2012
PubMed-ID: 23035213 | Reference-DOI: 10.1128/JVI.06975-11

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:101 , ASN A:111 , THR A:113 , ASN A:132 , ALA A:133 , TYR A:155 , LYS A:187 , TYR A:188 , SER A:190 , HOH A:432 , HOH A:454 , HOH A:507 , HOH A:514 , HOH A:515 , HOH A:521 , HOH A:534	BINDING SITE FOR RESIDUE MN0 A 301
2	AC2	SOFTWARE	MET A:168 , TYR A:175 , THR A:186 , ARG A:210 , GLU A:213	BINDING SITE FOR RESIDUE GOL A 302
3	AC3	SOFTWARE	SER A:134 , GLN A:135 , THR A:136 , TYR A:155 , HOH A:548 , HOH A:550 , HOH A:603	BINDING SITE FOR RESIDUE GOL A 303
4	AC4	SOFTWARE	TYR A:69 , HOH A:579	BINDING SITE FOR RESIDUE 1PE A 304

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

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
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Chain A from PDB  Type:PROTEIN  Length:161
 aligned with VP4_ROTRH | P12473 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:161
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
            VP4_ROTRH    64 VLDGPYQPTSFNPPVDYWMLLAPTAAGVVVEGTNNTDRWLATILVEPNVTSETRSYTLFGTQEQITIANASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTYNGETPNVTTKYYSTTNYDSVNMTAFCDFYIIPREEESTCTEYINNGL 224
               SCOP domains d3tb0a_ A: vp4 sialic acid binding domain                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eee.....eeeee.....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeee..hhhhheeee...eeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------S-------------------G---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tb0 A  64 VLDGPYQPTTFNPPVDYWMLLAPTAAGVVVEGTNNTDRWLATILVEPNVTSETRSYTLFGTQEQITIANASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTYNGETPNVTTKYYSTTNYDSVNMTAFCDFYIIPREEESTCTEYINNGL 224
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223

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 (VP4_ROTRH | P12473)

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.

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

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Description