1QJZ - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Title :   THREE DIMENSIONAL STRUCTURE OF PHYSALIS MOTTLE VIRUS: IMPLICATIONS FOR THE VIRAL ASSEMBLY

Authors :   S. S. Krishna, C. N. Hiremath, S. K. Munshi, D. Prahadeeswaran, M. Sastri, H. S. Savithri, M. R. N. Murthy

Date :   07 Jul 99 (Deposition) - 08 Jul 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.80

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

Keywords :   Virus, Coat Protein (Viral), Icosahedral Virus, Capsid Protein, Virion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. S. Krishna, C. N. Hiremath, S. K. Munshi, D. Prahadeeswaran, M. Sastri, H. S. Savithri, M. R. N. Murthy
Three Dimensional Structure Of Physalis Movirus: Implications For The Viral Assembly
J. Mol. Biol. V. 289 919 1999
PubMed-ID: 10369772 | Reference-DOI: 10.1006/JMBI.1999.2787
(for further references see the PDB file header)

Molecule 1 - COAT PROTEIN
	Biological Unit	:	ICOSAHEDRAL SHELL
	Chains	:	A, B, C
	Organism Common	:	PHMV
	Organism Scientific	:	PHYSALIS MOTTLE VIRUS
	Organism Taxid	:	72539
	Strain	:	IOWA
	Synonym	:	VIRION PROTEIN

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1QJZ)

(no "Site" information available for 1QJZ)

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

Asymmetric Unit

No.	Residues
1	Ile A:14	-	Pro A:15

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

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

(no "Exon" information available for 1QJZ)

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:179
 aligned with COAT_PHMV | P36351 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:179
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179         
            COAT_PHMV    10 KQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
               SCOP domains d1qjza_ A: Tymovirus coat protein                                                                                                                                                   SCOP domains
               CATH domains 1qjzA00 A:10-188  [code=2.60.120.20, no name defined]                                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......................eeeee..............eee...hhhhhh....eeeeeeeee................eeeee.......hhhhh......eee................hhhhh..eee.........eeeee..................eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qjz A  10 KQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179

Chain B from PDB  Type:PROTEIN  Length:188
 aligned with COAT_PHMV | P36351 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
            COAT_PHMV     1 MDSSEVVKVKQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
               SCOP domains d1qjzb_ B: Tymovirus coat protein                                                                                                                                                            SCOP domains
               CATH domains 1qjzB00 B:1-188  [code=2.60.120.20, no name defined]                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......................eeeeeee..............ee...hhhhhhhhh.eeeeeeeeeeeeeeehhhhhhh.......eee.....hhhhhhhh................eeeee.hhhhh..eee........eee....................eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qjz B   1 MDSSEVVKVKQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain C from PDB  Type:PROTEIN  Length:188
 aligned with COAT_PHMV | P36351 from UniProtKB/Swiss-Prot  Length:188

    Alignment length:188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        
            COAT_PHMV     1 MDSSEVVKVKQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
               SCOP domains d1qjzc_ C: Tymovirus coat protein                                                                                                                                                            SCOP domains
               CATH domains 1qjzC00 C:1-188  [code=2.60.120.20, no name defined]                                                                                                                                         CATH domains
           Pfam domains (1) -------Tymo_coat-1qjzC01 C:8-179                                                                                                                                                   --------- Pfam domains (1)
           Pfam domains (2) -------Tymo_coat-1qjzC02 C:8-179                                                                                                                                                   --------- Pfam domains (2)
           Pfam domains (3) -------Tymo_coat-1qjzC03 C:8-179                                                                                                                                                   --------- Pfam domains (3)
         Sec.struct. author ...............................eeeeeeeeee......eeeeee...hhhhhhhhh....eeeeeeeeee..hhhhhhh.eeeeeeeee.....hhhhhhhh...eeeee.....................eee........eeeeeee.............eeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qjz C   1 MDSSEVVKVKQASIPAPGSILSQPNTEQSPAIVLPFQFEATTFGTAETAAQVSLQTADPITKLTAPYRHAQIVECKAILTPTDLAVSNPLTVYLAWVPANSPATPTQILRVYGGQSFVLGGAISAAKTIEVPLNLDSVNRMLKDSVTYTDTPKLLAYSRAPTNPSKIPTASIQISGRIRLSKPMLIAN 188
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

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: Tymoviridae-like VP (7)

Protein domain: Tymovirus coat protein (5)

PHMV (Physalis mottle virus) [TaxId: 72539] (2)

1a	d1qjza_	A:
1b	d1qjzb_	B:
1c	d1qjzc_	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)

Phmv (Physalis mottle virus) (1)

1a	1qjzB00	B:1-188
1b	1qjzC00	C:1-188
1c	1qjzA00	A:10-188

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Viral_ssRNA_CP (106)

Family: Tymo_coat (4)

Physalis mottle virus (PhMV) (Belladonna mottle virus-Iowa) (3)

1a	Tymo_coat-1qjzC01	C:8-179
1b	Tymo_coat-1qjzC02	C:8-179
1c	Tymo_coat-1qjzC03	C:8-179

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (COAT_PHMV | P36351)

molecular function
	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
(no "Ligands, Modified Residues, Ions" information available for 1qjz)

	Sites
(no "Sites" information available for 1qjz)

	Cis Peptide Bonds
		Ile A:14 - Pro A:15	[ 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 \| Biol. Unit 1 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
	1qjz
		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
	COAT_PHMV \| P36351
		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
	COAT_PHMV \| P36351
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	COAT_PHMV \| P36351	:	1e57 2wws 2xpj

1e57	PHYSALIS MOTTLE VIRUS: EMPTY CAPSID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (1, 3)

Pfam Domains (1, 3)

Gene Ontology (4, 4)

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