2OV7 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   THE FIRST DOMAIN OF THE RIBOSOMAL PROTEIN L1 FROM THERMUS THERMOPHILUS

Authors :   V. Kljashtorny, S. Tishchenko, N. Nevskaya, S. Nikonov, N. Davydova, M. Garber

Date :   13 Feb 07 (Deposition) - 25 Dec 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Ribosomal Protein L1, Thermus Thermophilus (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Tishchenko, E. Nikonova, V. Kljashtorny, O. Kostareva, N. Nevskaya, W. Piendl, N. Davydova, V. Streltsov, M. Garber, S. Nikonov
Domain I Of Ribosomal Protein L1 Is Sufficient For Specific Rna Binding.
Nucleic Acids Res. V. 35 7389 2007
PubMed-ID: 17962298 | Reference-DOI: 10.1093/NAR/GKM898
(for further references see the PDB file header)

Molecule 1 - 50S RIBOSOMAL PROTEIN L1
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PDOM1TTHL1.4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2OV7)

(no "Site" information available for 2OV7)

(no "SS Bond" information available for 2OV7)

(no "Cis Peptide Bond" information available for 2OV7)

(no "SAP(SNP)/Variant" information available for 2OV7)

(no "PROSITE Motif" information available for 2OV7)

(no "Exon" information available for 2OV7)

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:134
 aligned with RL1_THETH | P27150 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:225
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     
            RL1_THETH     5 GKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 229
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh........hhhhhhhhhhhh.......eeeeeeee...........eeeee....-------------------------------------------------------------------------------------------.eeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhh..........eeeeeeee.....ee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ov7 A   4 GKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHG-------------------------------------------------------------------------------------------GRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 228
                                    13        23        33        43        53        63   |     -         -         -         -         -         -         -         -         -     | 163       173       183       193       203       213       223     
                                                                                          67                                                                                         159

Chain B from PDB  Type:PROTEIN  Length:133
 aligned with RL1_THETH | P27150 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:224
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225    
            RL1_THETH     6 KRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 229
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.......hhhhhhhhhhhh.......eeeeeee............eeeee....-------------------------------------------------------------------------------------------.eeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhh.............eeee......ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ov7 B   5 KRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHG-------------------------------------------------------------------------------------------GRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 228
                                    14        24        34        44        54        64  |      -         -         -         -         -         -         -         -         -    |  164       174       184       194       204       214       224    
                                                                                         67                                                                                         159

Chain C from PDB  Type:PROTEIN  Length:128
 aligned with RL1_THETH | P27150 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:219
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
            RL1_THETH    11 LLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 229
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Ribosomal_L1-2ov7C01 C:10-221                                                                                                                                                                                       ------- Pfam domains (1)
           Pfam domains (2) Ribosomal_L1-2ov7C02 C:10-221                                                                                                                                                                                       ------- Pfam domains (2)
           Pfam domains (3) Ribosomal_L1-2ov7C03 C:10-221                                                                                                                                                                                       ------- Pfam domains (3)
         Sec.struct. author ...........hhhhhhhhhhhhh......eeeeeeee...........eeee.....-------------------------------------------------------------------------------------------..eeee.....eeeeeeee...hhhhhhhhhhhhhhhhh...........eeeeeee.....eeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ov7 C  10 LLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHG-------------------------------------------------------------------------------------------GRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 228
                                    19        29        39        49        59       | -         -         -         -         -         -         -         -         -       159       169       179       189       199       209       219         
                                                                                    67                                                                                         159

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 2OV7)

(no "CATH Domain" information available for 2OV7)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ribosome_L1 (7)

Family: Ribosomal_L1 (7)

Thermus thermophilus (4)

1a	Ribosomal_L1-2ov7C01	C:10-221
1b	Ribosomal_L1-2ov7C02	C:10-221
1c	Ribosomal_L1-2ov7C03	C:10-221

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (RL1_THETH | P27150)

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.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	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:0015934	large ribosomal subunit	The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
	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.

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1i2a	L1 FROM METHANOCOCCUS JANNASCHII
1mzp	STRUCTURE OF THE L1 PROTUBERANCE IN THE RIBOSOME
1u63	L1-MRNA COMPLEX FROM METHANOCOCCUS JANNASCHII
1zho	L1 IN COMPLEX WITH MRNA AT 2.6 RESOLUTION
2hw8	L1-MRNA COMPLEX AT 2.1 RESOLUTION
2oum	THE FIRST DOMAIN OF THE RIBOSOMAL PROTEIN L1 FROM T. THERMOPHILUS AT 2.55A RESOLUTION.

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