1MJI | PR0083 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   DETAILED ANALYSIS OF RNA-PROTEIN INTERACTIONS WITHIN THE BACTERIAL RIBOSOMAL PROTEIN L5/5S RRNA COMPLEX

Authors :   A. Perederina, N. Nevskaya, O. Nikonov, A. Nikulin, P. Dumas, M. Yao, I. Tanaka, M. Garber, G. Gongadze, S. Nikonov

Date :   28 Aug 02 (Deposition) - 21 Jan 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Ribosomal Protein - 5S Rrna Complex, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Perederina, N. Nevskaya, O. Nikonov, A. Nikulin, P. Dumas, M. Yao, I. Tanaka, M. Garber, G. Gongadze, S. Nikonov
Detailed Analysis Of Rna-Protein Interactions Within The Bacterial Ribosomal Protein L5/5S Rrna Complex
Rna V. 8 1548 2002
PubMed-ID: 12515387
(for further references see the PDB file header)

Molecule 1 - 5S RRNA FRAGMENT
	Chains	:	C, D
	Engineered	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	IN VITRO TRANSCRIPTION

Molecule 2 - 50S RIBOSOMAL PROTEIN L5
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	K	2	Ligand/Ion	POTASSIUM ION
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG B:128 , ASN B:130 , THR B:161 , ALA B:163 , HOH B:219	BINDING SITE FOR RESIDUE MG B 201
2	AC2	SOFTWARE	ARG A:128 , ASN A:130 , THR A:161 , ALA A:163 , HOH C:211	BINDING SITE FOR RESIDUE MG A 202
3	AC3	SOFTWARE	C C:38 , A C:39 , C C:47 , U C:48	BINDING SITE FOR RESIDUE MG C 203
4	AC4	SOFTWARE	C D:38 , A D:39 , C D:47 , U D:48	BINDING SITE FOR RESIDUE MG D 204
5	AC5	SOFTWARE	U D:32 , HOH D:221	BINDING SITE FOR RESIDUE K D 205

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

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

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L5	PS00358	Ribosomal protein L5 signature.	RL5_THETH	60-76	2	A:60-76 B:60-76

(no "Exon" information available for 1MJI)

Asymmetric/Biological 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:180
 aligned with RL5_THETH | P41201 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:180
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182
            RL5_THETH     3 LDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFRK 182
               SCOP domains d1mjia_ A: Ribosomal protein L5                                                                                                                                                      SCOP domains
               CATH domains 1mjiA00 A:3-182  [code=3.30.1440.10, no name defined]                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhh..eeeeeeeee......hhhhhhhhhhhhhhhhh...eeee..............eeeeeeeehhhhhhhhhhhhhhh....................eeeeee...ee....ee........eeeeeee...hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------RIBOSOMAL_L5     ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mji A   3 LDVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRmWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGmDIAVVTTAETDEEARALLELLGFPFRK 182
                                    12        22        32        42        52        62        72        82        92      |102       112       122       132       142       152  |    162       172       182
                                                                                                                           99-MSE                                                 155-MSE

Chain B from PDB  Type:PROTEIN  Length:179
 aligned with RL5_THETH | P41201 from UniProtKB/Swiss-Prot  Length:182

    Alignment length:179
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173         
            RL5_THETH     4 DVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRMWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGMDIAVVTTAETDEEARALLELLGFPFRK 182
               SCOP domains d1mjib_ B: Ribosomal protein L5                                                                                                                                                     SCOP domains
               CATH domains 1mjiB00 B:4-182  [code=3.30.1440.10, no name defined]                                                                                                                               CATH domains
           Pfam domains (1) -----------------------Ribosomal_L5-1mjiB01 B:27-83                             ---Ribosomal_L5_C-1mjiB03 B:87-181                                                                - Pfam domains (1)
           Pfam domains (2) -----------------------Ribosomal_L5-1mjiB02 B:27-83                             ---Ribosomal_L5_C-1mjiB04 B:87-181                                                                - Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.........eeeeeeeeee.......hhhhhhhhhhhhhhh...eeee..............eeeeeeeehhhhhhhhhhhhhhh.....................eeeee................eeeeeeeeee...hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------RIBOSOMAL_L5     ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mji B   4 DVALKRKYYEEVRPELIRRFGYQNVWEVPRLEKVVINQGLGEAKEDARILEKAAQELALITGQKPAVTRAKKSISNFKLRKGMPIGLRVTLRRDRmWIFLEKLLNVALPRIRDFRGLNPNSFDGRGNYNLGLREQLIFPEITYDMVDALRGmDIAVVTTAETDEEARALLELLGFPFRK 182
                                    13        23        33        43        53        63        73        83        93     | 103       113       123       133       143       153 |     163       173         
                                                                                                                          99-MSE                                                 155-MSE

Chain C from PDB  Type:RNA  Length:34
                                                                  
                 1mji C  26 GGCACCUGACCCCAUGCCGAACUCAGAAGUGCCC  59
                                    35        45        55

Chain D from PDB  Type:RNA  Length:34
                                                                  
                 1mji D  26 GGCACCUGACCCCAUGCCGAACUCAGAAGUGCCC  59
                                    35        45        55

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: RL5-like (90)

Superfamily: RL5-like (90)

Family: Ribosomal protein L5 (82)

Protein domain: Ribosomal protein L5 (82)

Thermus thermophilus [TaxId: 274] (6)

1a	d1mjia_	A:
1b	d1mjib_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: 50s Ribosomal Protein L5; Chain: A, (78)

Homologous Superfamily: [code=3.30.1440.10, no name defined] (78)

Escherichia coli. Organism_taxid: 562. (1)

1a	1mjiB00	B:4-182
1b	1mjiA00	A:3-182

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Ribosomal_L5] (45)

Family: Ribosomal_L5 (45)

Thermus thermophilus (1)

1a	Ribosomal_L5-1mjiB01	B:27-83
1b	Ribosomal_L5-1mjiB02	B:27-83

Clan: no clan defined [family: Ribosomal_L5_C] (46)

Family: Ribosomal_L5_C (46)

Thermus thermophilus (1)

2a	Ribosomal_L5_C-1mjiB03	B:87-181
2b	Ribosomal_L5_C-1mjiB04	B:87-181

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (RL5_THETH | P41201)

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: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: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.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

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