1RLG | PR0108 - JenaLib

Title :   MOLECULAR BASIS OF BOX C/D RNA-PROTEIN INTERACTION: CO-CRYSTAL STRUCTURE OF THE ARCHAEAL SRNP INTIATION COMPLEX

Authors :   T. Moore, Y. Zhang, M. O. Fenley, H. Li

Date :   25 Nov 03 (Deposition) - 01 Jun 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Protein-Rna, Structural Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Moore, Y. Zhang, M. O. Fenley, H. Li
Molecular Basis Of Box C/D Rna-Protein Interactions; Cocrystal Structure Of Archaeal L7Ae And A Box C/D Rna.
Structure V. 12 807 2004
PubMed-ID: 15130473 | Reference-DOI: 10.1016/J.STR.2004.02.033
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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
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Chain A from PDB  Type:PROTEIN  Length:113
 aligned with RL7A_ARCFU | O29494 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:113
                                    16        26        36        46        56        66        76        86        96       106       116   
           RL7A_ARCFU     7 VPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQK 119
               SCOP domains d1rlga_ A: Ribosomal protein L7ae                                                                                 SCOP domains
               CATH domains 1rlgA00 A:7-119  [code=3.30.1330.30, no name defined]                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhheeeehhhhhhhhhh.....eeeee..........hhhhhhhhh...eeee.hhhhhhhhh.......eeeeeehhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------RIBOSOMAL_L7AE    ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 1rlg A   7 VPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQK 119
                                    16        26        36        46        56        66        76        86        96       106       116

Chain B from PDB  Type:PROTEIN  Length:117
 aligned with RL7A_ARCFU | O29494 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:117
                                    11        21        31        41        51        61        71        81        91       101       111       
           RL7A_ARCFU     2 YVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQ 118
               SCOP domains d1rlgb_ B: Ribosomal protein L7ae                                                                                     SCOP domains
               CATH domains 1rlgB00 B:2-118  [code=3.30.1330.30, no name defined]                                                                 CATH domains
           Pfam domains (1) -----------Ribosomal_L7Ae-1rlgB01 B:13-113                                                                      ----- Pfam domains (1)
           Pfam domains (2) -----------Ribosomal_L7Ae-1rlgB02 B:13-113                                                                      ----- Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhheeeehhhhhhhhhhh....eeeee..........hhhhhh......eeee.hhhhhhhhhh......eeeeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------RIBOSOMAL_L7AE    ----------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1rlg B   2 YVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRKELGSLVEKIKGLQ 118
                                    11        21        31        41        51        61        71        81        91       101       111

Chain C from PDB  Type:RNA  Length:25
                                                         
                 1rlg C   1 GCuCuGACCGAAAGGCGUGAuGAGC  25
                              | |   10        20|    
                              3-5BU            21-5BU
                                5-5BU

Chain D from PDB  Type:RNA  Length:25
                                                         
                 1rlg D   1 GCuCuGACCGAAAGGCGUGAuGAGC  25
                              | |   10        20|    
                              3-5BU            21-5BU
                                5-5BU

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 (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (14, 14)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RL7A_ARCFU | O29494)

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:0004526	ribonuclease P activity	Catalysis of the endonucleolytic cleavage of RNA, removing 5' extra nucleotides from tRNA precursor.
	GO:0003735	structural constituent of ribosome	The action of a molecule that contributes to the structural integrity of the ribosome.
biological process
	GO:0090501	RNA phosphodiester bond hydrolysis	The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
	GO:0090502	RNA phosphodiester bond hydrolysis, endonucleolytic	The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.
	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.
	GO:0001682	tRNA 5'-leader removal	Generation of the mature 5'-end of the tRNA, usually via an endonucleolytic cleavage by RNase P.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
	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.

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