1LAJ | PR0068 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE STRUCTURE OF TOMATO ASPERMY VIRUS BY X-RAY CRYSTALLOGRAPHY

Authors :   R. W. Lucas, S. B. Larson, M. A. Canady, A. Mcpherson

Date :   28 Mar 02 (Deposition) - 27 Nov 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

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

Keywords :   Anti-Parallel Beta Sheets, Jelly Roll, T=3 Icosahedral Virus, Protein-Rna Complex, Disulphide Bridge, Icosahedral Virus, Virus/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. W. Lucas, S. B. Larson, M. A. Canady, A. Mcpherson
The Structure Of Tomato Aspermy Virus By X-Ray Crystallography
J. Struct. Biol. V. 139 90 2002
PubMed-ID: 12406691 | Reference-DOI: 10.1016/S1047-8477(02)00561-0
(for further references see the PDB file header)

Molecule 1 - CAPSID PROTEIN
	Chains	:	A, B, C
	Organism Scientific	:	TOMATO ASPERMY VIRUS
	Organism Taxid	:	12315
	Strain	:	BLENCOWE

*Molecule 2 - 5'-R(APAPA)-3'**
	Chains	:	R
	Engineered	:	YES
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	R
Biological Unit 1 (60x)	:	A	B	C	R

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	MG	1	Ligand/Ion	MAGNESIUM ION
2	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (1, 60)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	PO4	60	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU B:175 , GLU C:175	BINDING SITE FOR RESIDUE MG B 2000

Asymmetric Unit

No.	Residues
1	A:64	-	A:106
2	B:64	-	B:106
3	C:64	-	C:106

(no "Cis Peptide Bond" information available for 1LAJ)

(no "SAP(SNP)/Variant" information available for 1LAJ)

(no "PROSITE Motif" information available for 1LAJ)

(no "Exon" information available for 1LAJ)

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:174
 aligned with CAPSD_TAV | P23627 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:175
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
            CAPSD_TAV    44 NIASSSAPSLQHPTFIASKKCRAGYTYTSLDVRPTRTEKDKSFGQRLIIPVPVSEYPKKKVSCVQVRLNPSPKFNSTIWVSLRRLDETTLLTSENVFKLFTDGLAAVLIYQHVPTGIQPNNKITFDMSNVGAEIGDMGKYALIVYSKDDVLEADEMVIHIDIEHQRIPSLQRSRC 218
               SCOP domains d1laja_ A: Cucumovirus coat protein                                                                                                                                             SCOP domains
               CATH domains 1lajA00 A:44-217 Positive standed ss RNA viruses, Chain A                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.................ee....ee.........eeeee.............eeeeeeeeeee.......eeeeee........hhhhhhhhhh....-.eee.............eee.....ee.hhhhh.eeeeee.........eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1laj A  44 NIASSSAPSLQHPTFIASKKCRAGYTYTSLDVRPTRTEKDKSFGQRLIIPVPVSEYPKKKVSCVQVRLNPSPKFNSTIWVSLRRLDETTLLTSENVFKLFTDGLA-VLIYQHVPTGIQPNNKITFDMSNVGAEIGDMGKYALIVYSKDDVLEADEMVIHIDIEHQRIPSASTLPV 217
                                    53        63        73        83        93       103       113       123       133       143    | |152       162       172       182       192       202       212     
                                                                                                                                  148 |                                                                    
                                                                                                                                    149

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with CAPSD_TAV | P23627 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:183
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215   
            CAPSD_TAV    36 TQQVNRLANIASSSAPSLQHPTFIASKKCRAGYTYTSLDVRPTRTEKDKSFGQRLIIPVPVSEYPKKKVSCVQVRLNPSPKFNSTIWVSLRRLDETTLLTSENVFKLFTDGLAAVLIYQHVPTGIQPNNKITFDMSNVGAEIGDMGKYALIVYSKDDVLEADEMVIHIDIEHQRIPSLQRSRC 218
               SCOP domains d1lajb_ B: Cucumovirus coat protein                                                                                                                                                     SCOP domains
               CATH domains 1lajB00 B:36-217 Positive standed ss RNA viruses, Chain A                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..................ee....ee.........eeeee.............eeeeeeeeeee.......eeeeee........hhhhhhhhhh....-.eee.............eee.....ee.hhhhh.eeeeee.........eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1laj B  36 TQQVNRLANIASSSAPSLQHPTFIASKKCRAGYTYTSLDVRPTRTEKDKSFGQRLIIPVPVSEYPKKKVSCVQVRLNPSPKFNSTIWVSLRRLDETTLLTSENVFKLFTDGLA-VLIYQHVPTGIQPNNKITFDMSNVGAEIGDMGKYALIVYSKDDVLEADEMVIHIDIEHQRIPSASTLPV 217
                                    45        55        65        75        85        95       105       115       125       135       145  | |  154       164       174       184       194       204       214   
                                                                                                                                          148 |                                                                    
                                                                                                                                            149

Chain C from PDB  Type:PROTEIN  Length:184
 aligned with CAPSD_TAV | P23627 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:185
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213     
            CAPSD_TAV    34 ALTQQVNRLANIASSSAPSLQHPTFIASKKCRAGYTYTSLDVRPTRTEKDKSFGQRLIIPVPVSEYPKKKVSCVQVRLNPSPKFNSTIWVSLRRLDETTLLTSENVFKLFTDGLAAVLIYQHVPTGIQPNNKITFDMSNVGAEIGDMGKYALIVYSKDDVLEADEMVIHIDIEHQRIPSLQRSRC 218
               SCOP domains d1lajc_ C: Cucumovirus coat protein                                                                                                                                                       SCOP domains
               CATH domains 1lajC00 C:34-217 Positive standed ss RNA viruses, Chain A                                                                                                                                 CATH domains
           Pfam domains (1) Cucumo_coat-1lajC01 C:34-211                                                                                       -                                                               ------ Pfam domains (1)
           Pfam domains (2) Cucumo_coat-1lajC02 C:34-211                                                                                       -                                                               ------ Pfam domains (2)
           Pfam domains (3) Cucumo_coat-1lajC03 C:34-211                                                                                       -                                                               ------ Pfam domains (3)
         Sec.struct. author ....hhhhhhhhhhhh..................eeeeeeee.........eeeee.............eeeeeeeeeee.......eeeeee........hhhhhhhhhh....-...............eeeee.....ee.hhhhh.eeeeee.........eeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1laj C  34 ALTQQVNRLANIASSSAPSLQHPTFIASKKCRAGYTYTSLDVRPTRTEKDKSFGQRLIIPVPVSEYPKKKVSCVQVRLNPSPKFNSTIWVSLRRLDETTLLTSENVFKLFTDGLA-VLIYQHVPTGIQPNNKITFDMSNVGAEIGDMGKYALIVYSKDDVLEADEMVIHIDIEHQRIPSASTLPV 217
                                    43        53        63        73        83        93       103       113       123       133       143    | |152       162       172       182       192       202       212     
                                                                                                                                            148 |                                                                    
                                                                                                                                              149

Chain R from PDB  Type:RNA  Length:3
                                   
                 1laj R 100 AAA 102

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: Bromoviridae-like VP (6)

Protein domain: Cucumovirus coat protein (5)

TAV (Tomato aspermy virus) [TaxId: 12315] (1)

1a	d1laja_	A:
1b	d1lajb_	B:
1c	d1lajc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Positive standed ss RNA viruses, Chain A (2)

Tomato aspermy virus. Organism_taxid: 12315. Strain: blencowe. (1)

1a	1lajB00	B:36-217
1b	1lajC00	C:34-217
1c	1lajA00	A:44-217

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Viral_ssRNA_CP (106)

Family: Cucumo_coat (1)

Tomato aspermy virus (TAV) (1)

1a	Cucumo_coat-1lajC01	C:34-211
1b	Cucumo_coat-1lajC02	C:34-211
1c	Cucumo_coat-1lajC03	C:34-211

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (CAPSD_TAV | P23627)

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:0019013	viral nucleocapsid	The complete protein-nucleic acid complex that is the packaged form of the genome in a virus particle.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

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1f15	CUCUMBER MOSAIC VIRUS USED AS MOLECULAR REPLACEMENT MODEL

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Ligands, Modified Residues, Ions (2, 2)

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SS Bonds (3, 3)

Cis Peptide Bonds (0, 0)

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