1F8V | PR0036 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   THE STRUCTURE OF PARIACOTO VIRUS REVEALS A DODECAHEDRAL CAGE OF DUPLEX RNA

Authors :   L. Tang, K. N. Johnson, L. A. Ball, T. Lin, M. Yeager, J. E. Johnson

Date :   05 Jul 00 (Deposition) - 06 Dec 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Nodavirus, Coat Protein, Nucleoprotein, Protein-Rna Interactions, Rna Duplex, Rna Cage, Gamma Polypeptide, Beta- Sandwich, Icosahedral Virus, Virus/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Tang, K. N. Johnson, L. A. Ball, T. Lin, M. Yeager, J. E. Johnson
The Structure Of Pariacoto Virus Reveals A Dodecahedral Cage Of Duplex Rna.
Nat. Struct. Biol. V. 8 77 2001
PubMed-ID: 11135676 | Reference-DOI: 10.1038/83089
(for further references see the PDB file header)

Molecule 1 - RNA
	Chains	:	R
	Organism Scientific	:	PARIACATO VIRUS
	Organism Taxid	:	103782

Molecule 2 - MATURE CAPSID PROTEIN BETA
	Chains	:	A, B, C
	Organism Scientific	:	PARIACATO VIRUS
	Organism Taxid	:	103782

Molecule 3 - MATURE CAPSID PROTEIN GAMMA
	Chains	:	D, E, F
	Organism Scientific	:	PARIACATO VIRUS
	Organism Taxid	:	103782

		1	2	3	4	5	6	7
Asymmetric Unit	:	A	B	C	D	E	F	R
Biological Unit 1 (60x)	:	A	B	C	D	E	F	R

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

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

Biological Unit 1 (1, 60)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	SO4	60	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:249 , ASP B:249 , ASP C:249 , MET D:401	BINDING SITE FOR RESIDUE SO4 C 500
2	AC2	SOFTWARE	ASP A:249 , GLU A:251 , ASP B:249 , ASP C:249 , GLU C:251	BINDING SITE FOR RESIDUE CA A 501

(no "SS Bond" information available for 1F8V)

Asymmetric Unit

No.	Residues
1	Thr A:202	-	Pro A:203
2	Ala A:204	-	Pro A:205
3	Thr B:202	-	Pro B:203
4	Ala B:204	-	Pro B:205
5	Thr C:202	-	Pro C:203
6	Ala C:204	-	Pro C:205

(no "SAP(SNP)/Variant" information available for 1F8V)

(no "PROSITE Motif" information available for 1F8V)

(no "Exon" information available for 1F8V)

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:355
 aligned with CAPSD_PAV | Q9J7Z0 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:355
                                    16        26        36        46        56        66        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     
            CAPSD_PAV     7 NRRNKARKVVSRSTALVPMAPASQRTGPAPRKPRKRNQALVRNPRLTDAGLAFLKCAFAAPDFSVDPGKGIPDNFHGRTLAIKDCNTTSVVFTPNTDTYIVVAPVPGFAYFRAEVAVGAQPTTFVGVPYPTYATNFGAGSQNGLPAVNNYSKFRYASMACGLYPTSNMMQFSGSVQVWRVDLNLSEAVNPAVTAITPAPGVFANFVDKRINGLRGIRPLAPRDNYSGNFIDGAYTFAFDKSTDFEWCDFVRSLEFSESNVLGAATAMKLLAPGGGTDTTLTGLGNVNTLVYKISTPTGAVNTAILRTWNCIELQPYTDSALFQFSGVSPPFDPLALECYHNLKMRFPVAVSSREN 361
               SCOP domains d1f8v.1 A:,D: Alphanodavirus capsid protein                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1f8vA00 A:7-361  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................................eee....hhhhhhhhhhhhh..................eeeeeeeeeeeeeee...eeeeeee.....eeeeeeee.......eeeeee..hhhhhhh............eeeeeeeeeeeeeee.........eeeeeee..eeeeeeeeeeee......eeeeeeeeeeehhhhh.......eeeee.hhheeee.............ee..eee...........eee.hhhhh...........eeeeeeee.....eeeeeeeeeeeeeee.....hhhhhee....hhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f8v A   7 NRRNKARKVVSRSTALVPMAPASQRTGPAPRKPRKRNQALVRNPRLTDAGLAFLKCAFAAPDFSVDPGKGIPDNFHGRTLAIKDCNTTSVVFTPNTDTYIVVAPVPGFAYFRAEVAVGAQPTTFVGVPYPTYATNFGAGSQNGLPAVNNYSKFRYASMACGLYPTSNMMQFSGSVQVWRVDLNLSEAVNPAVTAITPAPGVFANFVDKRINGLRGIRPLAPRDNYSGNFIDGAYTFAFDKSTDFEWCDFVRSLEFSESNVLGAATAMKLLAPGGGTDTTLTGLGNVNTLVYKISTPTGAVNTAILRTWNCIELQPYTDSALFQFSGVSPPFDPLALECYHNLKMRFPVAVSSREN 361
                                    16        26        36        46        56        66        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

Chain B from PDB  Type:PROTEIN  Length:313
 aligned with CAPSD_PAV | Q9J7Z0 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:313
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358   
            CAPSD_PAV    49 NPRLTDAGLAFLKCAFAAPDFSVDPGKGIPDNFHGRTLAIKDCNTTSVVFTPNTDTYIVVAPVPGFAYFRAEVAVGAQPTTFVGVPYPTYATNFGAGSQNGLPAVNNYSKFRYASMACGLYPTSNMMQFSGSVQVWRVDLNLSEAVNPAVTAITPAPGVFANFVDKRINGLRGIRPLAPRDNYSGNFIDGAYTFAFDKSTDFEWCDFVRSLEFSESNVLGAATAMKLLAPGGGTDTTLTGLGNVNTLVYKISTPTGAVNTAILRTWNCIELQPYTDSALFQFSGVSPPFDPLALECYHNLKMRFPVAVSSREN 361
               SCOP domains d1f8v.2 B:,E: Alphanodavirus capsid protein                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 1f8vB00 B:49-361  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh..............eeeeeeeeeeeeeee...eeeeeee.....eeeeeeee.......eeeeee..hhhhhhhhhhhh.......eeeeeeeeeeeeeee.........eeeeeee..eeeeeeeeeeee......eeeeeeeeeeehhhhh........eeee.hhheeee.............ee..eee...........eee.hhhhh...........eeeeeeee.....eeeeeeeeeeeeeee.....hhhhhee....hhhhhhhhhhhhhhh....hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f8v B  49 NPRLTDAGLAFLKCAFAAPDFSVDPGKGIPDNFHGRTLAIKDCNTTSVVFTPNTDTYIVVAPVPGFAYFRAEVAVGAQPTTFVGVPYPTYATNFGAGSQNGLPAVNNYSKFRYASMACGLYPTSNMMQFSGSVQVWRVDLNLSEAVNPAVTAITPAPGVFANFVDKRINGLRGIRPLAPRDNYSGNFIDGAYTFAFDKSTDFEWCDFVRSLEFSESNVLGAATAMKLLAPGGGTDTTLTGLGNVNTLVYKISTPTGAVNTAILRTWNCIELQPYTDSALFQFSGVSPPFDPLALECYHNLKMRFPVAVSSREN 361
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358

Chain C from PDB  Type:PROTEIN  Length:311
 aligned with CAPSD_PAV | Q9J7Z0 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:311
                                    60        70        80        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       350       360 
            CAPSD_PAV    51 RLTDAGLAFLKCAFAAPDFSVDPGKGIPDNFHGRTLAIKDCNTTSVVFTPNTDTYIVVAPVPGFAYFRAEVAVGAQPTTFVGVPYPTYATNFGAGSQNGLPAVNNYSKFRYASMACGLYPTSNMMQFSGSVQVWRVDLNLSEAVNPAVTAITPAPGVFANFVDKRINGLRGIRPLAPRDNYSGNFIDGAYTFAFDKSTDFEWCDFVRSLEFSESNVLGAATAMKLLAPGGGTDTTLTGLGNVNTLVYKISTPTGAVNTAILRTWNCIELQPYTDSALFQFSGVSPPFDPLALECYHNLKMRFPVAVSSREN 361
               SCOP domains d1f8v.3 C:,F: Alphanodavirus capsid protein                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1f8vC00 C:51-361  [code=2.60.120.20, no name defined]                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh..............eeeeeeeeeeeeeee...eeeeeee.....eeeeeeee.......eeeeee..hhhhhhh............eeeeeeeeeeeeeee.........eeeeeee..eeeeeeeeeeee......eeeeeeeeeeehhhhh........eeee.hhheeee.............ee..eee...........eee.hhhhh...........eeeeeeee.....eeeeeeeeeeeeeee...hhhhhhhee....hhhhhhhhhhhh.......hhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f8v C  51 RLTDAGLAFLKCAFAAPDFSVDPGKGIPDNFHGRTLAIKDCNTTSVVFTPNTDTYIVVAPVPGFAYFRAEVAVGAQPTTFVGVPYPTYATNFGAGSQNGLPAVNNYSKFRYASMACGLYPTSNMMQFSGSVQVWRVDLNLSEAVNPAVTAITPAPGVFANFVDKRINGLRGIRPLAPRDNYSGNFIDGAYTFAFDKSTDFEWCDFVRSLEFSESNVLGAATAMKLLAPGGGTDTTLTGLGNVNTLVYKISTPTGAVNTAILRTWNCIELQPYTDSALFQFSGVSPPFDPLALECYHNLKMRFPVAVSSREN 361
                                    60        70        80        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       350       360

Chain D from PDB  Type:PROTEIN  Length:26
 aligned with CAPSD_PAV | Q9J7Z0 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:40
                                   371       381       391       401
            CAPSD_PAV   362 SKFWEGVLRVLNQISGTLSVIPGPVGTISAGVHQLTGMYM 401
               SCOP domains d1f8v.1 A:,D:                            SCOP domains
               CATH domains 1f8vD00 D:362-401                        CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh....--------------........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 1f8v D 362 SKFWEGVLRVLNQISGTL--------------HQLTGMYM 401
                                   371       | -         -  |    401
                                           379            394

Chain E from PDB  Type:PROTEIN  Length:22
 aligned with CAPSD_PAV | Q9J7Z0 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:22
                                   371       381  
            CAPSD_PAV   362 SKFWEGVLRVLNQISGTLSVIP 383
               SCOP domains d1f8v.2 B:,E:          SCOP domains
               CATH domains 1f8vE00 E:362-383      CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 1f8v E 362 SKFWEGVLRVLNQISGTLSVIP 383
                                   371       381

Chain F from PDB  Type:PROTEIN  Length:22
 aligned with CAPSD_PAV | Q9J7Z0 from UniProtKB/Swiss-Prot  Length:401

    Alignment length:22
                                   371       381  
            CAPSD_PAV   362 SKFWEGVLRVLNQISGTLSVIP 383
               SCOP domains d1f8v.3 C:,F:          SCOP domains
               CATH domains 1f8vF00 F:362-383      CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 1f8v F 362 SKFWEGVLRVLNQISGTLSVIP 383
                                   371       381

Chain R from PDB  Type:RNA  Length:25
                                                         
                 1f8v R   1 UUUUUUUUUUUUUAAAAUUUUUUUU  25
                                    10        20

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: Nodaviridae-like VP (3)

Protein domain: Alphanodavirus capsid protein (3)

Pariacoto virus [TaxId: 103782] (1)

1a	d1f8v.1	A:,D:
1b	d1f8v.2	B:,E:
1c	d1f8v.3	C:,F:

(no "Pfam Domain" information available for 1F8V)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (CAPSD_PAV | Q9J7Z0)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
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:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	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.
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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	Cis Peptide Bonds
		Ala A:204 - Pro A:205	[ RasMol ]
		Ala B:204 - Pro B:205	[ RasMol ]
		Ala C:204 - Pro C:205	[ RasMol ]
		Thr A:202 - Pro A:203	[ RasMol ]
		Thr B:202 - Pro B:203	[ RasMol ]
		Thr C:202 - Pro C:203	[ RasMol ]

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	1f8v
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1nov	CRYSTAL STRUCTURE OF NODAMURA VIRUS
2bbv	CRYSTAL STRUCTURE OF BLACK BEETLE VIRUS

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

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