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NMR Structure - model 1 (Jmol Viewer)

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Title :   SOLUTION STRUCTURE AND BACKBONE DYNAMICS OF THE RIBOSOMAL PROTEIN S6WT

Authors :   A. Ohman, M. Oliveberg, T. Oman

Date :   10 Jun 09 (Deposition) - 22 Dec 09 (Release) - 26 Jan 10 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A  (20x)

Keywords :   S6, Solution Structure, Backbone Dynamics, Folding, Ribonucleoprotein, Ribosomal Protein, Rna-Binding, Rrna- Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Ohman, T. Oman, M. Oliveberg
Solution Structures And Backbone Dynamics Of The Ribosomal Protein S6 And Its Permutant P(54-55)
Protein Sci. V. 19 183 2010
PubMed-ID: 19937661 | Reference-DOI: 10.1002/PRO.298
(for further references see the PDB file header)

Molecule 1 - 30S RIBOSOMAL PROTEIN S6
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Variant	:	PLYSS
	Expression System Vector	:	PRSETA
	Gene	:	RPSF, RPS6
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	TS9


NMR Structure (20x)	:

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2KJV)

(no "Site" information available for 2KJV)

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

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

(no "SAP(SNP)/Variant" information available for 2KJV)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S6	PS01048	Ribosomal protein S6 signature.	RS6_THET8	44-53	1	A:44-53
1	RIBOSOMAL_S6	PS01048	Ribosomal protein S6 signature.	RS6_THETH	44-53	1	A:44-53

(no "Exon" information available for 2KJV)

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
	(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:101
 aligned with RS6_THET8 | Q5SLP8 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
            RS6_THET8     1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA 101
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2kjvA00 A:1-101  [code=3.30.70.60, no name defined]                                                   CATH domains
               Pfam domains -Ribosomal_S6-2kjvA01 A:2-93                                                                 -------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhhhh......eee..................eee......hhhhhhhhhhhhh......eeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------RIBOSOMAL_------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2kjv A   1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA 101
                                    10        20        30        40        50        60        70        80        90       100

Chain A from PDB  Type:PROTEIN  Length:101
 aligned with RS6_THETH | P23370 from UniProtKB/Swiss-Prot  Length:101

    Alignment length:101
                                    10        20        30        40        50        60        70        80        90       100 
            RS6_THETH     1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA 101
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2kjvA00 A:1-101  [code=3.30.70.60, no name defined]                                                   CATH domains
               Pfam domains -Ribosomal_S6-2kjvA01 A:2-93                                                                 -------- Pfam domains
         Sec.struct. author ...eeee.......hhhhhhhhhhhhhhhhhhh......eee..................eee......hhhhhhhhhhhhh......eeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------RIBOSOMAL_------------------------------------------------ PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 2kjv A   1 MRRYEVNIVLNPNLDQSQLALEKEIIQRALENYGARVEKVEELGLRRLAYPIAKDPQGYFLWYQVEMPEDRVNDLARELRIRDNVRRVMVVKSQEPFLANA 101
                                    10        20        30        40        50        60        70        80        90       100

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 '\|'

(no "SCOP Domain" information available for 2KJV)

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.60, no name defined] (93)

Thermus thermophilus. Organism_taxid: 274. (1)

2kjvA00

A:1-101

NMR Structure

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ribosomal_S6] (24)

Family: Ribosomal_S6 (24)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (18)

Ribosomal_S6-2kjvA01

A:2-93

NMR Structure(hide GO term definitions)

Chain A (RS6_THET8 | Q5SLP8)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Chain A (RS6_THETH | P23370)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0019843	rRNA binding	Interacting selectively and non-covalently with ribosomal RNA.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0030529	intracellular ribonucleoprotein complex	An intracellular macromolecular complex containing both protein and RNA molecules.
	GO:0005840	ribosome	An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

NMR Structure
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1ris	CRYSTAL STRUCTURE OF S6. RELATED ID: 16345 RELATED DB: BMRB SOLUTION STRUCTURE OF THE PERMUTANT S6P3.
2kjw	SOLUTION STRUCTURE OF THE PERMUTANT S6P3. RELATED ID: 16344 RELATED DB: BMRB SOLUTION STRUCTURE OF PARENT PROTEIN S6.

Description

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Ligands, Modified Residues, Ions (0, 0)

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