2TMV - JenaLib

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Title :   VISUALIZATION OF PROTEIN-NUCLEIC ACID INTERACTIONS IN A VIRUS. REFINED STRUCTURE OF INTACT TOBACCO MOSAIC VIRUS AT 2.9 ANGSTROMS RESOLUTION BY X-RAY FIBER DIFFRACTION

Authors :   G. Stubbs, R. Pattanayek, K. Namba

Date :   15 Sep 88 (Deposition) - 09 Jan 89 (Release) - 25 Aug 09 (Revision)

Method :   FIBER DIFFRACTION

Resolution :   2.90

Chains :   Asym. Unit : P,R
Biol. Unit 1: P,R  (49x)

Keywords :   Virus, Helical Virus, Virus/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Namba, R. Pattanayek, G. Stubbs
Visualization Of Protein-Nucleic Acid Interactions In A Virus. Refined Structure Of Intact Tobacco Mosaic Virus At 2. 9 A Resolution By X-Ray Fiber Diffraction.
J. Mol. Biol. V. 208 307 1989
PubMed-ID: 2769760 | Reference-DOI: 10.1016/0022-2836(89)90391-4
(for further references see the PDB file header)

*Molecule 1 - RNA (5'-R(PGPAPA)-3')**
	Chains	:	R
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - TMV COAT PROTEIN
	Chains	:	P
	Engineered	:	YES
	Organism Scientific	:	TOBACCO MOSAIC VIRUS
	Organism Taxid	:	12243
	Strain	:	VULGARE

		1	2
Asymmetric Unit	:	P	R
Biological Unit 1 (49x)	:	P	R

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

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

Biological Unit 1 (0, 0)

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

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP P:116 , G R:1 , A R:2 , A R:3 , HOH R:11 , HOH R:35	BINDING SITE FOR RESIDUE CA R 4

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

(no "Cis Peptide Bond" information available for 2TMV)

Asymmetric Unit (6, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CAPSD_TMV_001 *	T	29	I	CAPSD_TMV	---	---	P	T	28	I
2	UniProt	VAR_CAPSD_TMV_002 *	P	79	S	CAPSD_TMV	---	---	P	P	78	S
3	UniProt	VAR_CAPSD_TMV_003 *	E	96	D	CAPSD_TMV	---	---	P	E	95	D
4	UniProt	VAR_CAPSD_TMV_004 *	T	104	M	CAPSD_TMV	---	---	P	T	103	M
5	UniProt	VAR_CAPSD_TMV_005 *	G	138	R	CAPSD_TMV	---	---	P	G	137	R
6	UniProt	VAR_CAPSD_TMV_006 *	S	149	Y	CAPSD_TMV	---	---	P	S	148	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (6, 294)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CAPSD_TMV_001 *	T	29	I	CAPSD_TMV	---	---	P	T	28	I
2	UniProt	VAR_CAPSD_TMV_002 *	P	79	S	CAPSD_TMV	---	---	P	P	78	S
3	UniProt	VAR_CAPSD_TMV_003 *	E	96	D	CAPSD_TMV	---	---	P	E	95	D
4	UniProt	VAR_CAPSD_TMV_004 *	T	104	M	CAPSD_TMV	---	---	P	T	103	M
5	UniProt	VAR_CAPSD_TMV_005 *	G	138	R	CAPSD_TMV	---	---	P	G	137	R
6	UniProt	VAR_CAPSD_TMV_006 *	S	149	Y	CAPSD_TMV	---	---	P	S	148	Y
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2TMV)

(no "Exon" information available for 2TMV)

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 P from PDB  Type:PROTEIN  Length:154
 aligned with CAPSD_TMV | P69687 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    
            CAPSD_TMV     2 SYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTS 155
               SCOP domains d2tmvp_ P: Tobacco mosaic virus coat protein                                                                                                               SCOP domains
               CATH domains 2tmvP00 P:1-154  [code=1.20.120.70, no name defined]                                                                                                       CATH domains
               Pfam domains TMV_coat-2tmvP01 P:1-145                                                                                                                         --------- Pfam domains
         Sec.struct. author ........hhhhhh..eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...............eee..hhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------I-------------------------------------------------S----------------D-------M---------------------------------R----------Y------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tmv P   1 SYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTS 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain P from PDB  Type:PROTEIN  Length:154
 aligned with CAPSD_TMVB | P69688 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    
           CAPSD_TMVB     2 SYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTS 155
               SCOP domains d2tmvp_ P: Tobacco mosaic virus coat protein                                                                                                               SCOP domains
               CATH domains 2tmvP00 P:1-154  [code=1.20.120.70, no name defined]                                                                                                       CATH domains
               Pfam domains TMV_coat-2tmvP01 P:1-145                                                                                                                         --------- Pfam domains
         Sec.struct. author ........hhhhhh..eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...............eee..hhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------I-------------------------------------------------S----------------D-------M---------------------------------R----------Y------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tmv P   1 SYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTS 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain P from PDB  Type:PROTEIN  Length:154
 aligned with CAPSD_TMVKR | P69689 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:154
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151    
          CAPSD_TMVKR     2 SYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTS 155
               SCOP domains d2tmvp_ P: Tobacco mosaic virus coat protein                                                                                                               SCOP domains
               CATH domains 2tmvP00 P:1-154  [code=1.20.120.70, no name defined]                                                                                                       CATH domains
               Pfam domains TMV_coat-2tmvP01 P:1-145                                                                                                                         --------- Pfam domains
         Sec.struct. author ........hhhhhh..eehhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...............eee..hhhhhhhhhhhhhh........................hhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------I-------------------------------------------------S----------------D-------M---------------------------------R----------Y------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2tmv P   1 SYSITTPSQFVFLSSAWADPIELINLCTNALGNQFQTQQARTVVQRQFSEVWKPSPQVTVRFPDSDFKVYRYNAVLDPLVTALLGAFDTRNRIIEVENQANPTTAETLDATRRVDDATVAIRSAINNLIVELIRGTGSYNRSSFESSSGLVWTS 154
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain R from PDB  Type:RNA  Length:3
                                   
                 2tmv R   1 GAA   3

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 alpha proteins (14657)

Fold: Four-helical up-and-down bundle (308)

Superfamily: TMV-like viral coat proteins (8)

Family: TMV-like viral coat proteins (8)

Protein domain: Tobacco mosaic virus coat protein (5)

Tobacco mosaic virus, vulgare strain [TaxId: 12242] (5)

d2tmvp_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Four Helix Bundle (Hemerythrin (Met), subunit A) (300)

Homologous Superfamily: [code=1.20.120.70, no name defined] (5)

[unclassified] (3)

2tmvP00

P:1-154

Asymmetric Unit(hide GO term definitions)

Chain P (CAPSD_TMVB | P69688)

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:0019029	helical viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
	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.

Chain P (CAPSD_TMVKR | P69689)

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:0019029	helical viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
	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.

Chain P (CAPSD_TMV | P69687)

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:0019029	helical viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles; the subunits are arranged to form a protein helix with the genetic material contained within. Tobacco mosaic virus has such a capsid structure.
	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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	2tmv
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UniProtKB/Swiss-Prot
	CAPSD_TMV \| P69687	:	1ei7 3j06 3kml 4gqh 4udv
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(no "Related Entries Specified in the PDB File" available for 2TMV)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (6, 6)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (4, 12)

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