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Title :   STRUCTURE OF RIBOSOME MATURATION PROTEIN RIMM AND RIBOSOMAL PROTEIN S19

Authors :   T. Kaminishi, C. Takemoto, A. Tatsuguchi, M. Kawazoe, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   21 Apr 09 (Deposition) - 21 Apr 10 (Release) - 21 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Rimm N-Terminal Domain, Prc-Barrel Domain, Beta Barrels, Ribosome, 30S Ribosomal Subunit, Ribosome Biogenesis, 16S Rrna Processing, Ribosomal Protein, Rrna Binding, Protein- Protein Complex, Chaperone, Cytoplasm, Ribonucleoprotein, Rna-Binding, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Kaminishi, C. Takemoto, A. Tatsuguchi, M. Kawazoe, M. Shirouzu, S. Yokoyama
Structure Of Ribosome Maturation Protein Rimm And Ribosomal Protein S19
To Be Published
PubMed: search

Molecule 1 - RIBOSOME MATURATION FACTOR RIMM
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RIMM
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

Molecule 2 - 30S RIBOSOMAL PROTEIN S19
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	RPSS
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	UNX	1	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	UNX	-1	Ligand/Ion	UNKNOWN ATOM OR ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	UNX	1	Ligand/Ion	UNKNOWN ATOM OR ION

(no "Site" information available for 3A1P)

(no "SS Bond" information available for 3A1P)

(no "Cis Peptide Bond" information available for 3A1P)

(no "SAP(SNP)/Variant" information available for 3A1P)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S19	PS00323	Ribosomal protein S19 signature.	RS19_THET8	53-77	2	B:53-77 D:53-77

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S19	PS00323	Ribosomal protein S19 signature.	RS19_THET8	53-77	1	B:53-77 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S19	PS00323	Ribosomal protein S19 signature.	RS19_THET8	53-77	1	- D:53-77

(no "Exon" information available for 3A1P)

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
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Chain A from PDB  Type:PROTEIN  Length:161
 aligned with RIMM_THET8 | Q5SJH5 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
           RIMM_THET8     2 RLVEIGRFGAPYALKGGLRFRGEPVVLHLERVYVEGHGWRAIEDLYRVGEELVVHLAGVTDRTLAEALVGLRVYAEVADLPPLEEGRYYYFALIGLPVYVEGRQVGEVVDILDAGAQDVLIIRGVGERLRDRAERLVPLQAPYVRVEEGSIHVDPIPGLFD 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeee....eeeeee.hhhhhh.eeee...eeeeeeeeeee..eeeeee....hhhhhhh....eeeee.hhh........hhhhhh..eeee..eeeeeeeeeee....eeeeeee..........eeee.....eeee..eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1p A   2 RLVEIGRFGAPYALKGGLRFRGEPVVLHLERVYVEGHGWRAIEDLYRVGEELVVHLAGVTDRTLAEALVGLRVYAEVADLPPLEEGRYYYFALIGLPVYVEGRQVGEVVDILDAGAQDVLIIRGVGERLRDRAERLVPLQAPYVRVEEGSIHVDPIPGLFD 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain B from PDB  Type:PROTEIN  Length:85
 aligned with RS19_THET8 | Q5SHP2 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:85
                                    18        28        38        48        58        68        78        88     
           RS19_THET8     9 VFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK  93
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3a1pB00 B:9-93 30s Ribosomal Protein S19; Chain A                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh....eee.......hhhhh..eeeee....eeeee.hhhhh..hhhhhh........hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------RIBOSOMAL_S19            ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3a1p B   9 VFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK  93
                                    18        28        38        48        58        68        78        88

Chain C from PDB  Type:PROTEIN  Length:161
 aligned with RIMM_THET8 | Q5SJH5 from UniProtKB/Swiss-Prot  Length:162

    Alignment length:161
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161 
           RIMM_THET8     2 RLVEIGRFGAPYALKGGLRFRGEPVVLHLERVYVEGHGWRAIEDLYRVGEELVVHLAGVTDRTLAEALVGLRVYAEVADLPPLEEGRYYYFALIGLPVYVEGRQVGEVVDILDAGAQDVLIIRGVGERLRDRAERLVPLQAPYVRVEEGSIHVDPIPGLFD 162
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeee......eeeee.hhhhhh.eeee...eeeeeeeeeee..eeeeee....hhhhhhh....eeeee.hhh........hhhhhh..eeee..eeeeeeeeeee....eeeeeee...hhhhh.eeeee.....eeee..eeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3a1p C   2 RLVEIGRFGAPYALKGGLRFRGEPVVLHLERVYVEGHGWRAIEDLYRVGEELVVHLAGVTDRTLAEALVGLRVYAEVADLPPLEEGRYYYFALIGLPVYVEGRQVGEVVDILDAGAQDVLIIRGVGERLRDRAERLVPLQAPYVRVEEGSIHVDPIPGLFD 162
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain D from PDB  Type:PROTEIN  Length:85
 aligned with RS19_THET8 | Q5SHP2 from UniProtKB/Swiss-Prot  Length:93

    Alignment length:85
                                    18        28        38        48        58        68        78        88     
           RS19_THET8     9 VFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK  93
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3a1pD00 D:9-93 30s Ribosomal Protein S19; Chain A                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh....eee.......hhhhh..eeeee....eeeee.hhhhh..hhhhhh........hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------RIBOSOMAL_S19            ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 3a1p D   9 VFVDDHLLEKVLELNAKGEKRLIKTWSRRSTIVPEMVGHTIAVYNGKQHVPVYITENMVGHKLGEFAPTRTYRGHGKEAKATKKK  93
                                    18        28        38        48        58        68        78        88

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 3A1P)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 30s Ribosomal Protein S19; Chain A (104)

Homologous Superfamily: 30s Ribosomal Protein S19; Chain A (104)

Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. (12)

1a	3a1pB00	B:9-93
1b	3a1pD00	D:9-93

(no "Pfam Domain" information available for 3A1P)

Asymmetric Unit(hide GO term definitions)

Chain A,C (RIMM_THET8 | Q5SJH5)

molecular function
	GO:0043022	ribosome binding	Interacting selectively and non-covalently with any part of a ribosome.
biological process
	GO:0006364	rRNA processing	Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
	GO:0042274	ribosomal small subunit biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.
	GO:0042254	ribosome biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of ribosome subunits; includes transport to the sites of protein synthesis.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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 B,D (RS19_THET8 | Q5SHP2)

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.
	GO:0015935	small ribosomal subunit	The smaller of the two subunits of a ribosome.

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2dog	SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF THE T.THERMOPHILUS RIMM PROTEIN
2dyi	CRYSTAL STRUCTURE OF THE T. THERMOPHILUS RIMM PROTEIN
2e5l	CRYSTAL STRUCTURE OF THE T. THERMOPHILUS 30S RIBOSOMAL SUBUNIT CAPTURING TWO MOLECULES OF AN OLIGONUCLEOTIDE VIA THE SHINE-DALGARNO INTERACTION

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