1JVR - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   STRUCTURE OF THE HTLV-II MATRIX PROTEIN, NMR, 20 STRUCTURES

Authors :   A. M. Christensen, M. A. Massiah, B. G. Turner, W. I. Sundquist, M. F. Summers

Date :   03 Oct 96 (Deposition) - 12 Mar 97 (Release) - 24 Feb 09 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   Human T-Cell Leukemia Virus Type Ii Matrix Protein, Htlv-Ii Matrix Protein, Htlv-Ii Ma, Retroviral Matrix Protein, P17 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Christensen, M. A. Massiah, B. G. Turner, W. I. Sundquist, M. F. Summers
Three-Dimensional Structure Of The Htlv-Ii Matrix Protein And Comparative Analysis Of Matrix Proteins From The Different Classes Of Pathogenic Human Retroviruses.
J. Mol. Biol. V. 264 1117 1996
PubMed-ID: 9000634 | Reference-DOI: 10.1006/JMBI.1996.0700
(for further references see the PDB file header)

Molecule 1 - HUMAN T-CELL LEUKEMIA VIRUS TYPE II MATRIX PROTEIN
	Cell Line	:	BL21
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	WISP92-18
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Organism Scientific	:	HUMAN T-LYMPHOTROPIC VIRUS 2
	Organism Taxid	:	11909
	Synonym	:	HTLV-II MA, MA


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1JVR)

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

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

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

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

(no "Exon" information available for 1JVR)

NMR Structure

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
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Chain A from PDB  Type:PROTEIN  Length:137
 aligned with GAG_HTLV2 | P03346 from UniProtKB/Swiss-Prot  Length:433

    Alignment length:137
                             1                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       
            GAG_HTLV2     - -MGQIHGLSPTPIPKAPRGLSTHHWLNFLQAAYRLQPRPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPPYVEPTTTQCF 136
               SCOP domains d1jvra_ A: HTLV-II matrix protein                                                                                                         SCOP domains
               CATH domains 1jvrA00 A:0-136 Human T-cell Leukemia Virus Type Ii Matrix Protein                                                                        CATH domains
               Pfam domains -Gag_p19-1jvrA01 A:1-92                                                                      -------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhh......hhhhhhhhhhhhhhh........................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvr A   0 HMGQIHGLSPTPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPPYVEPTTTQCF 136
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain A from PDB  Type:PROTEIN  Length:137
 aligned with POL_HTLV2 | P03363 from UniProtKB/Swiss-Prot  Length:1461

    Alignment length:137
                             1                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       
            POL_HTLV2     - -MGQIHGLSPTPIPKAPRGLSTHHWLNFLQAAYRLQPRPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPPYVEPTTTQCF 136
               SCOP domains d1jvra_ A: HTLV-II matrix protein                                                                                                         SCOP domains
               CATH domains 1jvrA00 A:0-136 Human T-cell Leukemia Virus Type Ii Matrix Protein                                                                        CATH domains
               Pfam domains -Gag_p19-1jvrA01 A:1-92                                                                      -------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhh......hhhhhhhhhhhhhhh........................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvr A   0 HMGQIHGLSPTPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPPYVEPTTTQCF 136
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain A from PDB  Type:PROTEIN  Length:137
 aligned with PRO_HTLV2 | P03353 from UniProtKB/Swiss-Prot  Length:602

    Alignment length:137
                             1                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       
            PRO_HTLV2     - -MGQIHGLSPTPIPKAPRGLSTHHWLNFLQAAYRLQPRPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPPYVEPTTTQCF 136
               SCOP domains d1jvra_ A: HTLV-II matrix protein                                                                                                         SCOP domains
               CATH domains 1jvrA00 A:0-136 Human T-cell Leukemia Virus Type Ii Matrix Protein                                                                        CATH domains
               Pfam domains -Gag_p19-1jvrA01 A:1-92                                                                      -------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...hhhhhhhh......hhhhhhhhhhhhhhh........................................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jvr A   0 HMGQIHGLSPTPIPKAPRGLSTHHWLNFLQAAYRLQPGPSDFDFQQLRRFLKLALKTPIWLNPIDYSLLASLIPKGYPGRVVEIINILVKNQVSPSAPAAPVPTPICPTTTPPPPPPPSPEAHVPPPYVEPTTTQCF 136
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

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 '\|'

NMR Structure

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Retroviral matrix proteins (29)

Superfamily: Retroviral matrix proteins (29)

Family: HTLV-II matrix protein (1)

Protein domain: HTLV-II matrix protein (1)

Human T-cell leukemia virus type 2 [TaxId: 11909] (1)

d1jvra_

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Human T-cell Leukemia Virus Type II Matrix Protein (1)

Homologous Superfamily: Human T-cell Leukemia Virus Type Ii Matrix Protein (1)

Human t-lymphotropic virus 2. Organism_taxid: 11909. Cell_line: bl21. (1)

1jvrA00

A:0-136

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Matrix (11)

Family: Gag_p19 (1)

Human T-cell leukemia virus 2 (HTLV-2) (1)

Gag_p19-1jvrA01

A:1-92

NMR Structure(hide GO term definitions)

Chain A (POL_HTLV2 | P03363)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	GO:0004523	RNA-DNA hybrid ribonuclease activity	Catalysis of the endonucleolytic cleavage of RNA in RNA-DNA hybrids to 5'-phosphomonoesters.
	GO:0003964	RNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
	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:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0015074	DNA integration	The process in which a segment of DNA is incorporated into another, usually larger, DNA molecule such as a chromosome.
	GO:0006310	DNA recombination	Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	GO:0006278	RNA-dependent DNA biosynthetic process	A DNA biosynthetic process that uses RNA as a template for RNA-dependent DNA polymerases (e.g. reverse transcriptase) that synthesize the new strand.
	GO:0075713	establishment of integrated proviral latency	A process by which the virus integrates into the host genome and establishes as a stable provirus or prophage.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0039657	suppression by virus of host gene expression	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
	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.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	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.

Chain A (PRO_HTLV2 | P03353)

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:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0039657	suppression by virus of host gene expression	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of gene expression in the host organism. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Some protein processing events may be included when they are required to form an active form of a product from an inactive precursor form.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	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.

Chain A (GAG_HTLV2 | P03346)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	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.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	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.

NMR Structure
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