2VPL - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   THE STRUCTURE OF THE COMPLEX BETWEEN THE FIRST DOMAIN OF L1 PROTEIN FROM THERMUS THERMOPHILUS AND MRNA FROM METHANOCOCCUS JANNASCHII

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

Date :   01 Mar 08 (Deposition) - 23 Sep 08 (Release) - 23 Dec 08 (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 :   Ribosomal Protein, Rna/Protein Complex, Translation Regulation, Translation, Repressor, Rna-Binding, Trna-Binding, Rrna-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Tishchenko, V. Kljashtorny, O. Kostareva, N. Nevskaya, A. Nikulin, P. Gulak, W. Piendl, M. Garber, S. Nikonov
Domain Ii Of Thermus Thermophilus Ribosomal Protein L1 Hinders Recognition Of Its Mrna.
J. Mol. Biol. V. 383 301 2008
PubMed-ID: 18778715 | Reference-DOI: 10.1016/J.JMB.2008.08.058

Molecule 1 - 50S RIBOSOMAL PROTEIN L1
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	FIRST DOMAIN, RESIDUES 2-68,160-229
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

Molecule 2 - FRAGMENT OF MRNA FOR L1-OPERON CONTAINING REGULATOR L1-BINDING SITE
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

		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, 2)

No.	Name	Count	Type	Full Name
1	K	2	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:42 , THR A:216 , THR A:217 , U B:41 , U B:42	BINDING SITE FOR RESIDUE K A 1229
2	AC2	SOFTWARE	GLU C:42 , THR C:216 , THR C:217 , U D:41 , U D:42	BINDING SITE FOR RESIDUE K C 1229

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

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

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

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

(no "Exon" information available for 2VPL)

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:137
 aligned with RL1_THETH | P27150 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
            RL1_THETH     2 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 229
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhh......hhhhhhhhh..........eeeeeeee.....hhhhh.eeeee....-------------------------------------------------------------------------------------------.eeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhh..........eeeeeeee....eee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vpl A   1 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHG-------------------------------------------------------------------------------------------GRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 228
                                    10        20        30        40        50        60      |  -         -         -         -         -         -         -         -         -       160       170       180       190       200       210       220        
                                                                                             67                                                                                         159

Chain B from PDB  Type:RNA  Length:48
                                                                                
                 2vpl B   2 GGAGUGAAGGAGGCUCGCGAACUCGCGAAGCCGAGAAACUUCACUCCC  49
                                    11        21        31        41

Chain C from PDB  Type:PROTEIN  Length:137
 aligned with RL1_THETH | P27150 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221        
            RL1_THETH     2 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 229
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------Ribosomal_L1-2vplC01 C:8-221                                                                                                                                                                                          ------- Pfam domains (1)
           Pfam domains (2) -------Ribosomal_L1-2vplC02 C:8-221                                                                                                                                                                                          ------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhh.........hhhhhhhhh..........eeeeeeee...........eeeee....-------------------------------------------------------------------------------------------.eeeee.....eeeeeeee...hhhhhhhhhhhhhhhhhhh.........eeeeeeee.....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2vpl C   1 PKHGKRYRALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHG-------------------------------------------------------------------------------------------GRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS 228
                                    10        20        30        40        50        60      |  -         -         -         -         -         -         -         -         -       160       170       180       190       200       210       220        
                                                                                             67                                                                                         159

Chain D from PDB  Type:RNA  Length:46
                                                                              
                 2vpl D   2 GGAGUGAAGGAGGCUCGCGAUCGCGAAGCCGAGAAACUUCACUCCC  49
                                    11        21|       33        43      
                                              21|                         
                                               24

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 2VPL)

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Ribosome_L1 (7)

Family: Ribosomal_L1 (7)

Thermus thermophilus (4)

1a	Ribosomal_L1-2vplC01	C:8-221
1b	Ribosomal_L1-2vplC02	C:8-221

Asymmetric Unit(hide GO term definitions)

Chain A,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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2vpl)

Biological Units
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1ad2	RIBOSOMAL PROTEIN L1 MUTANT WITH SERINE 179 REPLACEDBY CYSTEINE
1eg0	FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME
1u63	THE STRUCTURE OF A RIBOSOMAL PROTEIN L1- MRNA COMPLEX
1zho	THE STRUCTURE OF A RIBOSOMAL PROTEIN L1 IN COMPLEX WITH MRNA
2j01	STRUCTURE OF THE THERMUS THERMOPHILUS 70S RIBOSOME COMPLEXED WITH MRNA, TRNA AND PAROMOMYCIN
487d	SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO- ELECTRONMICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMSRESOLUTION

Description

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Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (0, 0)

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Pfam Domains (1, 2)

Gene Ontology (9, 9)

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