1I6U | PR0047 - JenaLib

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Title :   RNA-PROTEIN INTERACTIONS: THE CRYSTAL STRUCTURE OF RIBOSOMAL PROTEIN S8/RRNA COMPLEX FROM METHANOCOCCUS JANNASCHII

Authors :   S. Tishchenko, A. Nikulin, N. Fomenkova, N. Nevskaya, O. Nikonov, P. Dumas, H. Moine, B. Ehresmann, C. Ehresmann, W. Piendl, V. Lamzin, M. Garber, S. Nikonov

Date :   05 Mar 01 (Deposition) - 03 Aug 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Protein-Rna Interactions, Ribosome, Ribosomal Protein S8, Rna, X-Ray Crystallography (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Tishchenko, A. Nikulin, N. Fomenkova, N. Nevskaya, O. Nikonov, P. Dumas, H. Moine, B. Ehresmann, C. Ehresmann, W. Piendl, V. Lamzin, M. Garber, S. Nikonov
Detailed Analysis Of Rna-Protein Interactions Within The Ribosomal Protein S8-Rrna Complex From The Archaeon Methanococcus Jannaschii.
J. Mol. Biol. V. 311 311 2001
PubMed-ID: 11478863 | Reference-DOI: 10.1006/JMBI.2001.4877
(for further references see the PDB file header)

Molecule 1 - 16S RRNA FRAGMENT
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	THE RRNA FRAGMENT WAS OBTAINED BY TRANSCRIPTION FROM SYNTHETIC DNA TEMPLATE USING T7 RNA POLYMERASE.
	Synthetic	:	YES

Molecule 2 - 30S RIBOSOMAL PROTEIN S8P
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	B834(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MJAS8
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:124 , ARG B:97 , HOH B:158 , HOH B:165 , G C:12	BINDING SITE FOR RESIDUE SO4 B 131
2	AC2	SOFTWARE	PHE B:79 , ARG B:92 , ARG B:124 , HOH B:144 , HOH B:179 , G D:12	BINDING SITE FOR RESIDUE SO4 B 132
3	AC3	SOFTWARE	THR B:107 , GLN B:108 , LEU B:121 , U D:15 , G D:23 , A D:24 , HOH D:51	BINDING SITE FOR RESIDUE SO4 D 38
4	AC4	SOFTWARE	THR A:107 , GLN A:108 , LEU A:121 , G C:23 , A C:24 , HOH C:91 , HOH C:100	BINDING SITE FOR RESIDUE SO4 C 38

(no "SS Bond" information available for 1I6U)

Asymmetric Unit

No.	Residues
1	Lys A:76	-	Pro A:77
2	Lys B:76	-	Pro B:77

(no "SAP(SNP)/Variant" information available for 1I6U)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S8	PS00053	Ribosomal protein S8 signature.	RS8_METJA	100-117	2	A:100-117 B:100-117

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S8	PS00053	Ribosomal protein S8 signature.	RS8_METJA	100-117	1	A:100-117 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S8	PS00053	Ribosomal protein S8 signature.	RS8_METJA	100-117	1	- B:100-117

(no "Exon" information available for 1I6U)

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:129
 aligned with RS8_METJA | P54041 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
            RS8_METJA     2 SLMDPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIEDGRAGIFKVELIGKINKCGAIKPRFPVKKFGYEKFEKRYLPARDFGILIVSTTQGVMSHEEAKKRGLGGRLLAYVY 130
               SCOP domains d1i6ua_ A: Ribosomal protein S8                                                                                                   SCOP domains
               CATH domains 1i6uA01 A:2-69  [code=3.30.1370.30, no name defined]                1i6uA02 A:70-130  [code=3.30.1490.10, no name defined]        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh.....eeee......eeeee.......eee.....ee....hhhhhhhhh......eeeeee..eeeehhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------RIBOSOMAL_S8      ------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i6u A   2 SLMDPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVmQDNGYIGEFEFIEDGRAGIFKVELIGKINKCGAIKPRFPVKKFGYEKFEKRYLPARDFGILIVSTTQGVmSHEEAKKRGLGGRLLAYVY 130
                                    11        21        31        41        51        61        71        81        91       101       111       121         
                                                                  41-MSE                                                               111-MSE

Chain B from PDB  Type:PROTEIN  Length:127
 aligned with RS8_METJA | P54041 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:127
                                    13        23        33        43        53        63        73        83        93       103       113       123       
            RS8_METJA     4 MDPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVMQDNGYIGEFEFIEDGRAGIFKVELIGKINKCGAIKPRFPVKKFGYEKFEKRYLPARDFGILIVSTTQGVMSHEEAKKRGLGGRLLAYVY 130
               SCOP domains d1i6ub_ B: Ribosomal protein S8                                                                                                 SCOP domains
               CATH domains 1i6uB01 B:4-69  [code=3.30.1370.30, no name defined]              1i6uB02 B:70-128  [code=3.30.1490.10, no name defined]     -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh.....eeee......eeeee.......eee.....ee....hhhhhhhhh......eeeeee..eeeehhhhhhh...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------RIBOSOMAL_S8      ------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1i6u B   4 MDPLANALNHISNCERVGKKVVYIKPASKLIGRVLKVmQDNGYIGEFEFIEDGRAGIFKVELIGKINKCGAIKPRFPVKKFGYEKFEKRYLPARDFGILIVSTTQGVmSHEEAKKRGLGGRLLAYVY 130
                                    13        23        33       |43        53        63        73        83        93       103       113       123       
                                                                41-MSE                                                               111-MSE

Chain C from PDB  Type:RNA  Length:37
                                                                     
                 1i6u C   1 GGGCCCGGUAAGUCUCUUCGGAGAUACUGCCGGGCCC  37
                                    10        20        30

Chain D from PDB  Type:RNA  Length:37
                                                                     
                 1i6u D   1 GGGCCCGGUAAGUCUCUUCGGAGAUACUGCCGGGCCC  37
                                    10        20        30

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 Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: Ribosomal protein S8 (57)

Superfamily: Ribosomal protein S8 (57)

Family: Ribosomal protein S8 (57)

Protein domain: Ribosomal protein S8 (57)

Methanococcus jannaschii [TaxId: 2190] (1)

1a	d1i6ua_	A:
1b	d1i6ub_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Dna Ligase; domain 1 (375)

Homologous Superfamily: [code=3.30.1490.10, no name defined] (105)

[unclassified] (2)

1a	1i6uB02	B:70-128
1b	1i6uA02	A:70-130

Topology: Ribosomal Protein S8; Chain: A, domain 1 (139)

Homologous Superfamily: [code=3.30.1370.30, no name defined] (105)

[unclassified] (2)

2a	1i6uA01	A:2-69
2b	1i6uB01	B:4-69

(no "Pfam Domain" information available for 1I6U)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RS8_METJA | P54041)

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.

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1bgz	THE NMR STRUCTURE OF S8 16S RRNA BINDING SITE FROM E. COLI

Description

Compounds

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Ligands, Modified Residues, Ions (2, 8)

Sites (4, 4)

SS Bonds (0, 0)

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