1QA6 | PR0015 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX

Authors :   G. L. Conn, D. E. Draper, E. E. Lattman, A. G. Gittis

Date :   15 Apr 99 (Deposition) - 25 May 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Ribosomal Rna, Tertiary Structur, E Rna-Protein Interaction, Minor Groove Binding, Antibiotic Binding, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. L. Conn, D. E. Draper, E. E. Lattman, A. G. Gittis
Crystal Structure Of A Conserved Ribosomal Protein-Rna Complex.
Science V. 284 1171 1999
PubMed-ID: 10325228 | Reference-DOI: 10.1126/SCIENCE.284.5417.1171
(for further references see the PDB file header)

Molecule 1 - 58 NUCLEOTIDE RIBOSOMAL RNA DOMAIN
	Chains	:	C, D
	Engineered	:	YES
	Fragment	:	NTS 1051-1108 FROM E. COLI 23S RRNA
	Mutation	:	YES
	Other Details	:	RNA SYNTHESIZED BY IN VITRO TRANSCRIPTION USING T7 RNA POLYMERASE
	Synthetic	:	YES

Molecule 2 - RIBOSOMAL PROTEIN L11
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11
	Organism Scientific	:	GEOBACILLUS STEAROTHERMOPHILUS
	Organism Taxid	:	1422

		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	MG	4	Ligand/Ion	MAGNESIUM ION
2	OS	4	Ligand/Ion	OSMIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	OS	-1	Ligand/Ion	OSMIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	OS	-1	Ligand/Ion	OSMIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	A C:107 , A C:139	BINDING SITE FOR RESIDUE MG C 202
2	AC2	SOFTWARE	G C:137	BINDING SITE FOR RESIDUE OS C 203
3	AC3	SOFTWARE	A D:107 , A D:139	BINDING SITE FOR RESIDUE MG D 206
4	AC4	SOFTWARE	G D:137	BINDING SITE FOR RESIDUE OS D 207

(no "SS Bond" information available for 1QA6)

(no "Cis Peptide Bond" information available for 1QA6)

(no "SAP(SNP)/Variant" information available for 1QA6)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L11	PS00359	Ribosomal protein L11 signature.	RL11_GEOSE	118-133	2	A:61-72 B:61-72

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L11	PS00359	Ribosomal protein L11 signature.	RL11_GEOSE	118-133	1	A:61-72 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L11	PS00359	Ribosomal protein L11 signature.	RL11_GEOSE	118-133	1	- B:61-72

(no "Exon" information available for 1QA6)

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:67
 aligned with RL11_GEOSE | P56210 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:67
                                    72        82        92       102       112       122       
           RL11_GEOSE    63 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGI 129
               SCOP domains d1qa6a_ A: Ribosomal protein L11, C-terminal domain                 SCOP domains
               CATH domains 1qa6A00 A:6-72  [code=1.10.10.250, no name defined]                 CATH domains
               Pfam domains ------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhh..................hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------RIBOSOMAL_L1 PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 1qa6 A   6 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGI  72
                                    15        25        35        45        55        65

Chain B from PDB  Type:PROTEIN  Length:67
 aligned with RL11_GEOSE | P56210 from UniProtKB/Swiss-Prot  Length:133

    Alignment length:67
                                    72        82        92       102       112       122       
           RL11_GEOSE    63 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGI 129
               SCOP domains d1qa6b_ B: Ribosomal protein L11, C-terminal domain                 SCOP domains
               CATH domains 1qa6B00 B:6-72  [code=1.10.10.250, no name defined]                 CATH domains
           Pfam domains (1) Ribosomal_L11-1qa6B01 B:6-72                                        Pfam domains (1)
           Pfam domains (2) Ribosomal_L11-1qa6B02 B:6-72                                        Pfam domains (2)
         Sec.struct. author ................................................................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------RIBOSOMAL_L1 PROSITE
                 Transcript ------------------------------------------------------------------- Transcript
                 1qa6 B   6 KTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARSMGI  72
                                    15        25        35        45        55        65

Chain C from PDB  Type:RNA  Length:58
                                                                                          
                 1qa6 C 101 GCCAGGAUGUAGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGU 158
                                   110       120       130       140       150

Chain D from PDB  Type:RNA  Length:58
                                                                                          
                 1qa6 D 101 GCCAGGAUGUAGGCUUAGAAGCAGCCAUCAUUUAAAGAAAGCGUAAUAGCUCACUGGU 158
                                   110       120       130       140       150

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: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Ribosomal protein L11, C-terminal domain (96)

Family: Ribosomal protein L11, C-terminal domain (96)

Protein domain: Ribosomal protein L11, C-terminal domain (96)

Bacillus stearothermophilus [TaxId: 1422] (8)

1a	d1qa6a_	A:
1b	d1qa6b_	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: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: [code=1.10.10.250, no name defined] (69)

[unclassified] (3)

1a	1qa6A00	A:6-72
1b	1qa6B00	B:6-72

Asymmetric Unit(hide GO term definitions)

Chain A,B (RL11_GEOSE | P56210)

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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(no "Related Entries Specified in the PDB File" available for 1QA6)

Description

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Ligands, Modified Residues, Ions (2, 8)

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SS Bonds (0, 0)

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