1OPO - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE STRUCTURE OF CARNATION MOTTLE VIRUS

Authors :   E. Morgunova, Z. Dauter, E. Fry, D. Stuart, V. Stel'Mashchuk, A. M. Mikhailov, K. S. Wilson, B. K. Vainshtein

Date :   06 Mar 03 (Deposition) - 01 Apr 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Plant Virus, Carmovirus, Virus/Viral Protein, X-Ray Diffraction, Tomato Bushy Stunt Virus, Icosahedral Virus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Morgunova, Z. Dauter, E. Fry, D. Stuart, V. Stel'Mashchuk, A. M. Mikhailov, K. S. Wilson, B. K. Vainshtein
The Atomic Structure Of Carnation Mottle Virus Capsid Protein
Febs Lett. V. 338 267 1994
PubMed-ID: 8307192 | Reference-DOI: 10.1016/0014-5793(94)80281-5
(for further references see the PDB file header)

Molecule 1 - COAT PROTEIN
	Chains	:	A, B, C
	Organism Scientific	:	CARNATION MOTTLE VIRUS
	Organism Taxid	:	11986

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 180)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	180	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:164 , THR A:165 , THR A:166 , GLY A:169 , LYS B:244	BINDING SITE FOR RESIDUE SO4 A 500
2	AC2	SOFTWARE	PRO B:164 , THR B:165 , THR B:166 , LYS C:244 , LYS C:281	BINDING SITE FOR RESIDUE SO4 B 501
3	AC3	SOFTWARE	LYS A:244 , PRO C:163 , PRO C:164 , THR C:165 , THR C:166 , GLY C:169	BINDING SITE FOR RESIDUE SO4 C 502
4	AC4	SOFTWARE	ASP B:158 , ASP B:161 , ASN C:128 , ASP C:200	BINDING SITE FOR RESIDUE CA B 503

(no "SS Bond" information available for 1OPO)

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

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

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_CARMV	139-164	3	A:139-164 B:139-164 C:139-164

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_CARMV	139-164	180	A:139-164 B:139-164 C:139-164

(no "Exon" information available for 1OPO)

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:267
 aligned with CAPSD_CARMV | P04383 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:267
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       
          CAPSD_CARMV    82 SMTMSKTELLSTVKGTTGVIPSFEDWVVSPRNVAVFPQLSLLATNFNKYRITALTVKYSPACSFETNGRVALGFNDDASDTPPTTKVGFYDLGKHVETAAQTAKDLVIPVDGKTRFIRDSASDDAKLVDFGRIVLSTYGFDKADTVVGELFIQYTIVLSDPTKTAKISQASNDKVSDGPTYVVPSVNGNELQLRVVAAGKWCIIVRGTVEGGFTKPTLIGPGISGDVDYESARPIAVCELVTQMEGQILKITKTSAEQPLQWVVYRM 348
               SCOP domains d1opoa_ A: Carmovirus coat protein                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1opoA01 A:82-245  [code=2.60.120.20, no name defined]                                                                                                               ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.......eeeeeee.......hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeee.........hhhhhhh..eeeeee....eeeee......ee.......hhhhhh.eeeeeeee.......eeeeeeeeeeeeeeee.......ee..hhhhh....eeeeee..eeeeee...eeeeeeee..........eee...eeeeeeee....eeeeeeee....eeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------ICOSAH_VIR_COAT_S         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1opo A  82 SMTMSKTELLSTVKGTTGVIPSFEDWVVSPRNVAVFPQLSLLATNFNKYRITALTVKYSPACSFETNGRVALGFNDDASDTPPTTKVGFYDLGKHVETAAQTAKDLVIPVDGKTRFIRDSASDDAKLVDFGRIVLSTYGFDKADTVVGELFIQYTIVLSDPTKTAKISQASNDKVSDGPTYVVPSVNGNELQLRVVAAGKWCIIVRGTVEGGFTKPTLIGPGISGDVDYESARPIAVCELVTQMEGQILKITKTSAEQPLQWVVYRM 348
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341

Chain B from PDB  Type:PROTEIN  Length:267
 aligned with CAPSD_CARMV | P04383 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:267
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       
          CAPSD_CARMV    82 SMTMSKTELLSTVKGTTGVIPSFEDWVVSPRNVAVFPQLSLLATNFNKYRITALTVKYSPACSFETNGRVALGFNDDASDTPPTTKVGFYDLGKHVETAAQTAKDLVIPVDGKTRFIRDSASDDAKLVDFGRIVLSTYGFDKADTVVGELFIQYTIVLSDPTKTAKISQASNDKVSDGPTYVVPSVNGNELQLRVVAAGKWCIIVRGTVEGGFTKPTLIGPGISGDVDYESARPIAVCELVTQMEGQILKITKTSAEQPLQWVVYRM 348
               SCOP domains d1opob_ B: Carmovirus coat protein                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1opoB01 B:82-245  [code=2.60.120.20, no name defined]                                                                                                               ------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee........eee..........hhhhhhhhh.eeeeeeeeeeeeeee........eeeeeee..................eeeeee....eeeee......ee.......hhhhhh..eeeeeee.......eeeeeeeeeeeeeeee.......ee..hhhhh....eeeeee..eeeeee...eeeeeeee..........eee...eeeeeeee....eeeeeeee....eeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------ICOSAH_VIR_COAT_S         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1opo B  82 SMTMSKTELLSTVKGTTGVIPSFEDWVVSPRNVAVFPQLSLLATNFNKYRITALTVKYSPACSFETNGRVALGFNDDASDTPPTTKVGFYDLGKHVETAAQTAKDLVIPVDGKTRFIRDSASDDAKLVDFGRIVLSTYGFDKADTVVGELFIQYTIVLSDPTKTAKISQASNDKVSDGPTYVVPSVNGNELQLRVVAAGKWCIIVRGTVEGGFTKPTLIGPGISGDVDYESARPIAVCELVTQMEGQILKITKTSAEQPLQWVVYRM 348
                                    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341

Chain C from PDB  Type:PROTEIN  Length:268
 aligned with CAPSD_CARMV | P04383 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:268
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340        
          CAPSD_CARMV    81 KSMTMSKTELLSTVKGTTGVIPSFEDWVVSPRNVAVFPQLSLLATNFNKYRITALTVKYSPACSFETNGRVALGFNDDASDTPPTTKVGFYDLGKHVETAAQTAKDLVIPVDGKTRFIRDSASDDAKLVDFGRIVLSTYGFDKADTVVGELFIQYTIVLSDPTKTAKISQASNDKVSDGPTYVVPSVNGNELQLRVVAAGKWCIIVRGTVEGGFTKPTLIGPGISGDVDYESARPIAVCELVTQMEGQILKITKTSAEQPLQWVVYRM 348
               SCOP domains d1opoc_ C: Carmovirus coat protein                                                                                                                                                                                                                                           SCOP domains
               CATH domains 1opoC01 C:81-245  [code=2.60.120.20, no name defined]                                                                                                                ------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Viral_coat-1opoC01 C:81-246                                                                                                                                           ---Carmo_coat_C-1opoC04 C:250-348                                                                      Pfam domains (1)
           Pfam domains (2) Viral_coat-1opoC02 C:81-246                                                                                                                                           ---Carmo_coat_C-1opoC05 C:250-348                                                                      Pfam domains (2)
           Pfam domains (3) Viral_coat-1opoC03 C:81-246                                                                                                                                           ---Carmo_coat_C-1opoC06 C:250-348                                                                      Pfam domains (3)
         Sec.struct. author ..eeeeeeeeeeeee.......eeeeeee.......hhhhhhhhh...eeeeeeeeeeeee........eeeeeee.........hhhhhhh..eeeeee....eeeee......ee.......hhhhhh.eeeeeeee.......eeeeeeeeeeeee..........ee...........eeeeee..eeeeee...eeeeeeee..........eee...eeeeeeee....eeeeeeee....eeeeee........eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------ICOSAH_VIR_COAT_S         ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1opo C  81 KSMTMSKTELLSTVKGTTGVIPSFEDWVVSPRNVAVFPQLSLLATNFNKYRITALTVKYSPACSFETNGRVALGFNDDASDTPPTTKVGFYDLGKHVETAAQTAKDLVIPVDGKTRFIRDSASDDAKLVDFGRIVLSTYGFDKADTVVGELFIQYTIVLSDPTKTAKISQASNDKVSDGPTYVVPSVNGNELQLRVVAAGKWCIIVRGTVEGGFTKPTLIGPGISGDVDYESARPIAVCELVTQMEGQILKITKTSAEQPLQWVVYRM 348
                                    90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340

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: Carmovirus coat protein (1)

CarMV (Carnation mottle virus) [TaxId: 11986] (1)

1a	d1opoa_	A:
1b	d1opob_	B:
1c	d1opoc_	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)

CaRNAtion mottle virus. Organism_taxid: 11986 (1)

1a	1opoC01	C:81-245
1b	1opoA01	A:82-245
1c	1opoB01	B:82-245

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Viral_ssRNA_CP (106)

Family: Viral_coat (12)

Carnation mottle virus (CarMV) (1)

1a	Viral_coat-1opoC01	C:81-246
1b	Viral_coat-1opoC02	C:81-246
1c	Viral_coat-1opoC03	C:81-246

Clan: no clan defined [family: Carmo_coat_C] (1)

Family: Carmo_coat_C (1)

Carnation mottle virus (CarMV) (1)

2a	Carmo_coat_C-1opoC04	C:250-348
2b	Carmo_coat_C-1opoC05	C:250-348
2c	Carmo_coat_C-1opoC06	C:250-348

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (CAPSD_CARMV | P04383)

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
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Biological Unit
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2tbv	STRUCTURE OF TOMATO BUSHY STUNT VIRUS. V. COAT PROTEIN SEQUENCE DETERMINATION AND ITS STRUCTURAL IMPLICATIONS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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