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Description

Title :   THE STRUCTURE OF RIBOSOMAL PROTEIN S5 REVEALS SITES OF INTERACTION WITH 16S RRNA

Authors :   V. Ramakrishnan, S. W. White

Date :   30 Aug 93 (Deposition) - 31 Jan 94 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Ribosomal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. Ramakrishnan, S. W. White
The Structure Of Ribosomal Protein S5 Reveals Sites Of Interaction With 16S Rrna.
Nature V. 358 768 1992
PubMed-ID: 1508272 | Reference-DOI: 10.1038/358768A0
(for further references see the PDB file header)

Compounds

Molecule 1 - RIBOSOMAL PROTEIN S5
	Chains	:	A
	Engineered	:	YES
	Expression System Gene	:	BACILLUS STEAROTHERMOPHILUS
	Gene	:	BACILLUS STEAROTHERMOPHILUS
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (0, 0)

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

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	SPR	AUTHOR	ARG A:20 , VAL A:21 , ALA A:22 , LYS A:23 , VAL A:24 , VAL A:25 , LYS A:26 , GLY A:27 , GLY A:28 , ARG A:29 , ARG A:30 , LEU A:31 , ARG A:32	PROPOSED SITES FOR INTERACTION WITH 16S R-RNA
2	STR	AUTHOR	GLY A:104 , ARG A:112	PROPOSED SITES FOR INTERACTION WITH 16S R-RNA

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

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

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (2, 2)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S5_DSRBD	PS50881	S5 double stranded RNA-binding domain profile.	RS5_GEOSE	11-74	1	A:11-74
2	RIBOSOMAL_S5	PS00585	Ribosomal protein S5 signature.	RS5_GEOSE	28-60	1	A:28-60

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	S5_DSRBD	PS50881	S5 double stranded RNA-binding domain profile.	RS5_GEOSE	11-74	2	A:11-74
2	RIBOSOMAL_S5	PS00585	Ribosomal protein S5 signature.	RS5_GEOSE	28-60	2	A:28-60

Exons (0, 0)

(no "Exon" information available for 1PKP)

Sequences/Alignments

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:145
 aligned with RS5_GEOSE | P02357 from UniProtKB/Swiss-Prot  Length:166

    Alignment length:145
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143     
            RS5_GEOSE     4 INPNKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIEDAKKNLIEVPIVGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSNTPINMVRATFDGLKQLK 148
               SCOP domains d1pkpa2 A:4-77 Ribosomal S5 protein, N-terminal domain                    d1pkpa1 A:78-148 Ribosomal protein S5, C-terminal domain                SCOP domains
               CATH domains 1pkpA01 A:4-73  [code=3.30.160.20, no name defined]                   1pkpA02 A:74-148  [code=3.30.230.10, no name defined]                       CATH domains
               Pfam domains ------Ribosomal_S5-1pkpA01 A:10-76                                       --------Ribosomal_S5_C-1pkpA02 A:85-148                                  Pfam domains
         Sec.struct. author ......eeeeeeeeeee...........eeeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhh.............eeeeeee..eeeeeee..........hhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------S5_DSRBD  PDB: A:11-74 UniProt: 11-74                           -------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------RIBOSOMAL_S5  PDB: A:28-60       ---------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1pkp A   4 INPNKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIEDAKKNLIEVPIVGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSNTPINMVRATFDGLKQLK 148
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143

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 '\|'

Classification and Annotation

SCOP Domains (2, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: dsRBD-like (111)

Superfamily: dsRNA-binding domain-like (98)

Family: Ribosomal S5 protein, N-terminal domain (61)

Protein domain: Ribosomal S5 protein, N-terminal domain (61)

Bacillus stearothermophilus [TaxId: 1422] (1)

d1pkpa2

A:4-77

Fold: Ribosomal protein S5 domain 2-like (306)

Superfamily: Ribosomal protein S5 domain 2-like (306)

Family: Translational machinery components (150)

Protein domain: Ribosomal protein S5, C-terminal domain (61)

Bacillus stearothermophilus [TaxId: 1422] (1)

d1pkpa1

A:78-148

CATH Domains (2, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Double Stranded RNA Binding Domain (204)

Homologous Superfamily: [code=3.30.160.20, no name defined] (122)

Geobacillus stearothermophilus. Organism_taxid: 1422. (1)

1pkpA01

A:4-73

Topology: Ribosomal Protein S5; domain 2 (189)

Homologous Superfamily: [code=3.30.230.10, no name defined] (170)

Geobacillus stearothermophilus. Organism_taxid: 1422. (1)

1pkpA02

A:74-148

Pfam Domains (2, 2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DSRM (45)

Family: Ribosomal_S5 (18)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (1)

Ribosomal_S5-1pkpA01

A:10-76

Clan: S5 (103)

Family: Ribosomal_S5_C (18)

Geobacillus stearothermophilus (Bacillus stearothermophilus) (1)

Ribosomal_S5_C-1pkpA02

A:85-148

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (RS5_GEOSE | P02357)

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:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	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.
	GO:0015935	small ribosomal subunit	The smaller of the two subunits of a ribosome.

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Related Entries

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UniProtKB/Swiss-Prot
	RS5_GEOSE \| P02357	:	1dv4 1eg0 1qd7

Related Entries Specified in the PDB File

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