2I2S - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE PORCINE CRW-8 ROTAVIRUS VP8* CARBOHYDRATE-RECOGNISING DOMAIN

Authors :   H. Blanchard

Date :   16 Aug 06 (Deposition) - 03 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

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

Reference :   H. Blanchard, X. Yu, B. S. Coulson, M. Von Itzstein
Insight Into Host Cell Carbohydrate-Recognition By Human An Porcine Rotavirus From Crystal Structures Of The Virion Spike Associated Carbohydrate-Binding Domain (Vp8*)
J. Mol. Biol. V. 367 1215 2007
PubMed-ID: 17306299 | Reference-DOI: 10.1016/J.JMB.2007.01.028
(for further references see the PDB file header)

Molecule 1 - OUTER CAPSID PROTEIN VP4
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PGEX-VP8*(64-224)
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	VP8* DOMAIN
	Organism Scientific	:	PORCINE ROTAVIRUS
	Organism Taxid	:	10913
	Strain	:	STRAIN CRW-8
	Synonym	:	SPIKE PROTEIN

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 11)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MNA	3	Ligand/Ion	2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
3	MPD	2	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	NA	2	Ligand/Ion	SODIUM ION
5	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MNA	2	Ligand/Ion	2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	NA	-1	Ligand/Ion	SODIUM ION
5	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 5)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MNA	1	Ligand/Ion	2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID
3	MPD	1	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	NA	-1	Ligand/Ion	SODIUM ION
5	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:90 , VAL A:91 , TYR A:119 , ASN A:120 , HOH A:6104 , HOH A:6108	BINDING SITE FOR RESIDUE SO4 A 3000
02	AC2	SOFTWARE	MNA A:1000 , TYR B:69 , GLN B:70 , HOH B:6040 , HOH B:6103	BINDING SITE FOR RESIDUE SO4 B 3001
03	AC3	SOFTWARE	ASP A:142 , GLY A:156 , TYR A:165 , THR A:176 , TYR A:177 , HOH A:6006	BINDING SITE FOR RESIDUE NA A 6000
04	AC4	SOFTWARE	ASP B:142 , GLY B:156 , TYR B:165 , THR B:176 , TYR B:177 , HOH B:6055	BINDING SITE FOR RESIDUE NA B 6001
05	AC5	SOFTWARE	ARG A:101 , HIS A:155 , TYR A:188 , TYR A:189 , SER A:190 , HOH A:6018 , HOH A:6024 , HOH A:6059 , HOH A:6076 , PRO B:68 , GLN B:70 , SO4 B:3001	BINDING SITE FOR RESIDUE MNA A 1000
06	AC6	SOFTWARE	THR A:78 , SER A:129 , GLU A:131 , THR A:153 , GLN A:154 , HOH A:6008 , HOH A:6053 , HOH A:6086 , HOH A:6087 , HOH A:6115 , HOH A:6122 , HOH A:6136 , ASN B:111 , GLN B:113	BINDING SITE FOR RESIDUE MNA A 1001
07	AC7	SOFTWARE	ARG B:101 , TYR B:188 , TYR B:189 , SER B:190 , GOL B:4001 , HOH B:6028 , HOH B:6029 , HOH B:6039 , HOH B:6056 , HOH B:6098	BINDING SITE FOR RESIDUE MNA B 1002
08	AC8	SOFTWARE	LEU A:64 , ARG B:210	BINDING SITE FOR RESIDUE GOL B 4000
09	AC9	SOFTWARE	MNA B:1002 , HOH B:6039	BINDING SITE FOR RESIDUE GOL B 4001
10	BC1	SOFTWARE	GLN A:124 , THR B:136 , HOH B:6086 , HOH B:6091 , HOH B:6117	BINDING SITE FOR RESIDUE MPD B 5000
11	BC2	SOFTWARE	PHE A:122 , LYS A:145 , PRO A:148	BINDING SITE FOR RESIDUE MPD A 5001

(no "SS Bond" information available for 2I2S)

Asymmetric Unit

No.	Residues
1	Gly A:67	-	Pro A:68
2	Thr A:181	-	Pro A:182
3	Gly B:67	-	Pro B:68
4	Thr B:181	-	Pro B:182

(no "SAP(SNP)/Variant" information available for 2I2S)

(no "PROSITE Motif" information available for 2I2S)

(no "Exon" information available for 2I2S)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	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 VP4_ROTP3 | P0C6Y8 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:174
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            VP4_ROTP3    51 GAGETNDSTTVEPLLDGPYRPTTFNPPTSYWVLLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGSYTQHGPLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTLFCDFYIIPRNQEEKCTEYINHGL 224
               SCOP domains d2           i2sa_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains 2i           2sA00 A:62-224  [code=2.60.120.200, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------..eeee..eee.....eeeeee....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeee..hhhhheeee..eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i2s A  62 GS-----------LLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGNYTQHGSLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 224
                             |       -   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
                             |          64                                                                                                                                                                
                            63

Chain A from PDB  Type:PROTEIN  Length:163
 aligned with VP4_ROTP5 | P11114 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:174
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            VP4_ROTP5    51 GAGETNDSTTVEPLLDGPYQPTTFNPPTSYWVLLAPTVEGVIIQGTNNTDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSTTTPTGSYTQHGPLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSATNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 224
               SCOP domains d2           i2sa_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains 2i           2sA00 A:62-224  [code=2.60.120.200, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------..eeee..eee.....eeeeee....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeee..hhhhheeee..eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i2s A  62 GS-----------LLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGNYTQHGSLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 224
                             |       -   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
                            63          64

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with VP4_ROTP3 | P0C6Y8 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:174
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            VP4_ROTP3    51 GAGETNDSTTVEPLLDGPYRPTTFNPPTSYWVLLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGSYTQHGPLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTLFCDFYIIPRNQEEKCTEYINHGL 224
               SCOP domains d2           i2sb_ B: automated matches                                                                                                                                        SCOP domains
               CATH domains 2i           2sB00 B:62-224  [code=2.60.120.200, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------..eeee..eee.....eeeeee....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeee..hhhhheeee..eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i2s B  62 GS-----------LLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGNYTQHGSLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 224
                             |       -   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
                            63          64

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with VP4_ROTP5 | P11114 from UniProtKB/Swiss-Prot  Length:776

    Alignment length:174
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
            VP4_ROTP5    51 GAGETNDSTTVEPLLDGPYQPTTFNPPTSYWVLLAPTVEGVIIQGTNNTDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSTTTPTGSYTQHGPLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSATNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 224
               SCOP domains d2           i2sb_ B: automated matches                                                                                                                                        SCOP domains
               CATH domains 2i           2sB00 B:62-224  [code=2.60.120.200, no name defined]                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..-----------..eeee..eee.....eeeeee....eeeeeee.....eeeeeee...eeeeeeeeee..eeeeeeeee.....eeeeeeee.......eeeeeeee....eeeeee..eeeeeeee....eeeeee..hhhhheeee..eeeeee..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i2s B  62 GS-----------LLDGPYQPTTFNPPTSYWILLAPTVEGVVIQGTNNIDRWLATILIEPNVQTTNRIYNLFGQQVTLSVENTSQTQWKFIDVSKTTPTGNYTQHGSLFSTPKLYAVMKFSGRIYTYNGTTPNATTGYYSTTNYDTVNMTSFCDFYIIPRNQEEKCTEYINHGL 224
                             |       -   |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220    
                            63          64

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	-	→ 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: All beta proteins (24004)

Fold: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: vp4 sialic acid binding domain (10)

Protein domain: automated matches (4)

Rotavirus c [TaxId: 10913] (1)

1a	d2i2sa_	A:
1b	d2i2sb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.200, no name defined] (421)

Porcine rotavirus. Organism_taxid: 10913. Strain: strain crw-8. (1)

1a	2i2sA00	A:62-224
1b	2i2sB00	B:62-224

(no "Pfam Domain" information available for 2I2S)

Asymmetric Unit(hide GO term definitions)

Chain A,B (VP4_ROTP3 | P0C6Y8)

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.

Chain A,B (VP4_ROTP5 | P11114)

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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		Thr A:181 - Pro A:182	[ RasMol ]
		Thr B:181 - Pro B:182	[ RasMol ]

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	VP4_ROTP3 \| P0C6Y8	:	3sis 3sit 3tay

Description

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Ligands, Modified Residues, Ions (5, 11)

Sites (11, 11)

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