2TBV - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   STRUCTURE OF TOMATO BUSHY STUNT VIRUS. V. COAT PROTEIN SEQUENCE DETERMINATION AND ITS STRUCTURAL IMPLICATIONS

Authors :   S. C. Harrison

Date :   22 Jun 84 (Deposition) - 20 Jul 84 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (60x)

Keywords :   Virus, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Hopper, S. C. Harrison, R. T. Sauer
Structure Of Tomato Bushy Stunt Virus. V. Coat Protein Sequence Determination And Its Structural Implications
J. Mol. Biol. V. 177 701 1984
PubMed-ID: 6481803 | Reference-DOI: 10.1016/0022-2836(84)90045-7
(for further references see the PDB file header)

Molecule 1 - TOMATO BUSHY STUNT VIRUS
	Chains	:	A, B, C
	Engineered	:	YES
	Organism Scientific	:	TOMATO BUSHY STUNT VIRUS
	Organism Taxid	:	12145

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (60x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 6)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:153 , ASP A:225 , ASP C:183 , ASP C:186	BINDING SITE FOR RESIDUE CA C 388
2	AC2	SOFTWARE	ASP B:183 , ASP B:186 , ASP C:153 , ASP C:225	BINDING SITE FOR RESIDUE CA C 389
3	AC3	SOFTWARE	ASP A:183 , ASP A:186 , ASP B:153 , ASP B:225 , GLN B:267	BINDING SITE FOR RESIDUE CA A 388
4	AC4	SOFTWARE	ASP A:153 , GLN A:267 , ASP C:181	BINDING SITE FOR RESIDUE CA A 389
5	AC5	SOFTWARE	ASP B:181 , ASP B:186 , GLN C:267	BINDING SITE FOR RESIDUE CA B 388
6	AC6	SOFTWARE	ASP A:181 , GLN B:267	BINDING SITE FOR RESIDUE CA A 390

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

Asymmetric Unit

No.	Residues
1	Gly A:289	-	Pro A:290
2	Leu A:358	-	Pro A:359
3	Gly B:289	-	Pro B:290
4	Leu B:358	-	Pro B:359
5	Gly C:289	-	Pro C:290
6	Leu C:358	-	Pro C:359

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICOSAH_VIR_COAT_S	PS00555	Plant viruses icosahedral capsid proteins 'S' region signature.	CAPSD_TBSVB	164-189	3	A:164-189 B:164-189 C:164-189

Biological Unit 1 (1, 180)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ICOSAH_VIR_COAT_S	PS00555	Plant viruses icosahedral capsid proteins 'S' region signature.	CAPSD_TBSVB	164-189	180	A:164-189 B:164-189 C:164-189

(no "Exon" information available for 2TBV)

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:287
 aligned with CAPSD_TBSVB | P11795 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:288
                                 108                                                                                                                                                                                                                                                                                        
                               107 |                                                                                                                                                                                                                                                                                        
                                 | 110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380        
          CAPSD_TBSVB   102 GSVTVT-HREYLTQVNNSSGFVVNGGIVGNLLQLNPSNGTLFSWLPAIASNFDQYSFNSVVLHYVPLCGTTEVGRVALYFDKDSQDPEPADRVELANFGVLKETAPWAEAMLRIPTDKVKRYCNDSATVDQKLIDLGQLGIATYGGAGTNAVGDVFISYSVTLYFPQPTNTLLSTRRLDLTGSLADATGPGYLVLTRTPTVLTHTFRVTGTFNLSGGLRCLTSLTLGATGAVVINDILAIDNVGTASAYFLNCTVSSLPATVTFTTTGISSATVNVVRGTRANVVNLL 388
               SCOP domains d2tbva_ A: Tombusvirus coat protein                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2tbvA00 A:101-387  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeee..eeeee...................hhhhhhhhh.eeeeeeeeeeeeee.....eeeeeeeee.........hhhhhhhhheeeee.....eeeee.......................eeeeeeee....eeeeeeeeeeeeeee...........eeee...eee......eeeeeee..eeeeeee..eeeeeeeeee.....eeeee.eeeeeeeeeeee...eeeeeeeeeee....eeeeee....eeeeeee.-......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------ICOSAH_VIR_COAT_S         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2tbv A 101 GGVTVTSHREYLTQVNNSSGFVVNGGIVGNSLQLNPSNGTLFSWLPALASNFDQYSFNSVVLDYVPLCGTTEVGRVALYFDKDSQDPEPADRVELANFGVLKETAPWAEAMLRIPTDKVKRYCNDSATVDQKLIDLGQLGIATYGGAGADAVGELFLARSVTLYFPQPTNTLLSSKRLDLTGSLADATGPGYLVLTRTPTVLTHTFRATGTFNLSGGLRCLTSLTLGATGAVVINDILAIDNVGTASDYFLNCTVSSLPATVTFTVSGVAAGILLVGR-ARANVVNLL 387
                                   110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       379        
                                                                                                                                                                                                                                                                                                               378 |        
                                                                                                                                                                                                                                                                                                                 379

Chain B from PDB  Type:PROTEIN  Length:287
 aligned with CAPSD_TBSVB | P11795 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:288
                                 108                                                                                                                                                                                                                                                                                        
                               107 |                                                                                                                                                                                                                                                                                        
                                 | 110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380        
          CAPSD_TBSVB   102 GSVTVT-HREYLTQVNNSSGFVVNGGIVGNLLQLNPSNGTLFSWLPAIASNFDQYSFNSVVLHYVPLCGTTEVGRVALYFDKDSQDPEPADRVELANFGVLKETAPWAEAMLRIPTDKVKRYCNDSATVDQKLIDLGQLGIATYGGAGTNAVGDVFISYSVTLYFPQPTNTLLSTRRLDLTGSLADATGPGYLVLTRTPTVLTHTFRVTGTFNLSGGLRCLTSLTLGATGAVVINDILAIDNVGTASAYFLNCTVSSLPATVTFTTTGISSATVNVVRGTRANVVNLL 388
               SCOP domains d2tbvb_ B: Tombusvirus coat protein                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2tbvB00 B:101-387  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeeeeeeeeee..eeeee...................hhhhhhhhh.eeeeeeeeeeeeee.....eeeeeeeee.........hhhhhhhhheeeee.....eeeee.......................eeeeeeee....eeeeeeeeeeeeeee...........eeee...eee......eeeeeee..eeeeeee..eeeeeeeeee.....eeeee.eeeeeeeeeeee...eeeeeeeeeee....eeeeee....eeeeeee.-......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------ICOSAH_VIR_COAT_S         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2tbv B 101 GGVTVTSHREYLTQVNNSSGFVVNGGIVGNSLQLNPSNGTLFSWLPALASNFDQYSFNSVVLDYVPLCGTTEVGRVALYFDKDSQDPEPADRVELANFGVLKETAPWAEAMLRIPTDKVKRYCNDSATVDQKLIDLGQLGIATYGGAGADAVGELFLARSVTLYFPQPTNTLLSSKRLDLTGSLADATGPGYLVLTRTPTVLTHTFRATGTFNLSGGLRCLTSLTLGATGAVVINDILAIDNVGTASDYFLNCTVSSLPATVTFTVSGVAAGILLVGR-ARANVVNLL 387
                                   110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       379        
                                                                                                                                                                                                                                                                                                               378 |        
                                                                                                                                                                                                                                                                                                                 379

Chain C from PDB  Type:PROTEIN  Length:321
 aligned with CAPSD_TBSVB | P11795 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:322
                                                                   108                                                                                                                                                                                                                                                                                        
                                                                 107 |                                                                                                                                                                                                                                                                                        
                                    77        87        97       107 |     116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386  
          CAPSD_TBSVB    68 IITHVGGVGGSIMAPVAVSRQLVGSKPKFTGRTSGSVTVT-HREYLTQVNNSSGFVVNGGIVGNLLQLNPSNGTLFSWLPAIASNFDQYSFNSVVLHYVPLCGTTEVGRVALYFDKDSQDPEPADRVELANFGVLKETAPWAEAMLRIPTDKVKRYCNDSATVDQKLIDLGQLGIATYGGAGTNAVGDVFISYSVTLYFPQPTNTLLSTRRLDLTGSLADATGPGYLVLTRTPTVLTHTFRVTGTFNLSGGLRCLTSLTLGATGAVVINDILAIDNVGTASAYFLNCTVSSLPATVTFTTTGISSATVNVVRGTRANVVNLL 388
               SCOP domains d2tbvc_ C: Tombusvirus coat protein                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2tbvC00 C:67-387  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) -------Viral_coat-2tbvC01 C:74-270                                                                                                                                                                          ---------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------Viral_coat-2tbvC02 C:74-270                                                                                                                                                                          ---------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -------Viral_coat-2tbvC03 C:74-270                                                                                                                                                                          ---------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ...........................eee......eeeeeeeeeeeeeee..eeeee...................hhhhhhhhh.eeeeeeeeeeeeee.....eeeeeeeee.........hhhhhhhhheeeee.....eeeee.......................eeeeeeee....eeeeeeeeeeeeeee...........eeee...eee......eeeeeee..eeeeeee..eeeeeeeeee.....eeeee.eeeeeeeeeeee...eeeeeeeeeee....eeeeee....eeeeeee.-......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------ICOSAH_VIR_COAT_S         ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tbv C  67 IITHVGGVGGSIMAPVAVSRQLVGSKPKFTGRTSGGVTVTSHREYLTQVNNSSGFVVNGGIVGNSLQLNPSNGTLFSWLPALASNFDQYSFNSVVLDYVPLCGTTEVGRVALYFDKDSQDPEPADRVELANFGVLKETAPWAEAMLRIPTDKVKRYCNDSATVDQKLIDLGQLGIATYGGAGADAVGELFLARSVTLYFPQPTNTLLSSKRLDLTGSLADATGPGYLVLTRTPTVLTHTFRATGTFNLSGGLRCLTSLTLGATGAVVINDILAIDNVGTASDYFLNCTVSSLPATVTFTVSGVAAGILLVGR-ARANVVNLL 387
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376 | |   385  
                                                                                                                                                                                                                                                                                                                                                 378 |        
                                                                                                                                                                                                                                                                                                                                                   379

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: All beta proteins (24004)

Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) (278)

Superfamily: Positive stranded ssRNA viruses (163)

Family: Tombusviridae-like VP (13)

Protein domain: Tombusvirus coat protein (1)

TBSV (Tomato bushy stunt virus) [TaxId: 12145] (1)

1a	d2tbva_	A:
1b	d2tbvb_	B:
1c	d2tbvc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: [code=2.60.120.20, no name defined] (133)

Tomato bushy stunt virus. Organism_taxid: 12145 (1)

1a	2tbvA00	A:101-387
1b	2tbvB00	B:101-387
1c	2tbvC00	C:67-387

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Viral_ssRNA_CP (106)

Family: Viral_coat (12)

Tomato bushy stunt virus (strain BS-3) (TBSV) (1)

1a	Viral_coat-2tbvC01	C:74-270
1b	Viral_coat-2tbvC02	C:74-270
1c	Viral_coat-2tbvC03	C:74-270

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (CAPSD_TBSVB | P11795)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
cellular component
	GO:0039617	T=3 icosahedral viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=3 symmetry. The T=3 capsid is composed of 12 pentameric and 20 hexameric capsomeres.
	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:0019012	virion	The complete fully infectious extracellular virus particle.

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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:289 - Pro A:290	[ RasMol ]
		Gly B:289 - Pro B:290	[ RasMol ]
		Gly C:289 - Pro C:290	[ RasMol ]
		Leu A:358 - Pro A:359	[ RasMol ]
		Leu B:358 - Pro B:359	[ RasMol ]
		Leu C:358 - Pro C:359	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2tbv
		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
	CAPSD_TBSVB \| P11795
		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

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
	CAPSD_TBSVB \| P11795
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 2TBV)

(no "Related Entries Specified in the PDB File" available for 2TBV)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File