3V7Q - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF B. SUBTILIS YLXQ AT 1.55 A RESOLUTION

Authors :   N. J. Baird, J. Zhang, T. Hamma, A. R. Ferre-D'Amare

Date :   21 Dec 11 (Deposition) - 07 Mar 12 (Release) - 18 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.55

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   L7Ae Superfamily, K-Turn Binding, K-Turn Rna, Hypothetical Ribosomal Protein, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. J. Baird, J. Zhang, T. Hamma, A. R. Ferre-D'Amare
Ybxf And Ylxq Are Bacterial Homologs Of L7Ae And Bind K-Turns But Not K-Loops.
Rna V. 18 759 2012
PubMed-ID: 22355167 | Reference-DOI: 10.1261/RNA.031518.111

Molecule 1 - PROBABLE RIBOSOMAL PROTEIN YLXQ
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	BSU16620, RPLGA, YLXQ, YMXC
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CIT	3	Ligand/Ion	CITRIC ACID
2	K	2	Ligand/Ion	POTASSIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	K	-1	Ligand/Ion	POTASSIUM ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	K	-1	Ligand/Ion	POTASSIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:7 , ARG A:31 , LYS A:55 , TYR A:58 , TYR A:59 , HOH A:583 , LYS B:194	BINDING SITE FOR RESIDUE CIT A 201
2	AC2	SOFTWARE	GLY A:22 , VAL A:82 , VAL A:83 , HOH A:567	BINDING SITE FOR RESIDUE K A 202
3	AC3	SOFTWARE	ASN A:47 , HOH A:516 , ARG B:131 , LYS B:155 , TYR B:158 , TYR B:159 , HOH B:1071 , PHE C:207	BINDING SITE FOR RESIDUE CIT B 901
4	AC4	SOFTWARE	GLY B:122 , ARG B:181 , VAL B:182	BINDING SITE FOR RESIDUE K B 902
5	AC5	SOFTWARE	PHE B:107 , ARG C:231 , LYS C:255 , TYR C:259	BINDING SITE FOR RESIDUE CIT C 401

(no "SS Bond" information available for 3V7Q)

(no "Cis Peptide Bond" information available for 3V7Q)

(no "SAP(SNP)/Variant" information available for 3V7Q)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L7AE	PS01082	Ribosomal protein L7Ae signature.	YLXQ_BACSU	56-73	3	A:56-73 B:156-173 C:256-273

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L7AE	PS01082	Ribosomal protein L7Ae signature.	YLXQ_BACSU	56-73	1	A:56-73 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L7AE	PS01082	Ribosomal protein L7Ae signature.	YLXQ_BACSU	56-73	1	- B:156-173 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_L7AE	PS01082	Ribosomal protein L7Ae signature.	YLXQ_BACSU	56-73	1	- - C:256-273

(no "Exon" information available for 3V7Q)

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:97
 aligned with YLXQ_BACSU | P32729 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:97
                                    12        22        32        42        52        62        72        82        92       
           YLXQ_BACSU     3 GMEWFPLLGLANRARKVVSGEDLVIKEIRNARAKLVLLTEDASSNTAKKVTDKCNYYKVPYKKVESRAVLGRSIGKEARVVVAVTDQGFANKLISLL  99
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeehhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhh......eeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------RIBOSOMAL_L7AE    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3v7q A   3 GMEWFPLLGLANRARKVVSGEDLVIKEIRNARAKLVLLTEDASSNTAKKVTDKCNYYKVPYKKVESRAVLGRSIGKEARVVVAVTDQGFANKLISLL  99
                                    12        22        32        42        52        62        72        82        92

Chain B from PDB  Type:PROTEIN  Length:97
 aligned with YLXQ_BACSU | P32729 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:97
                                    12        22        32        42        52        62        72        82        92       
           YLXQ_BACSU     3 GMEWFPLLGLANRARKVVSGEDLVIKEIRNARAKLVLLTEDASSNTAKKVTDKCNYYKVPYKKVESRAVLGRSIGKEARVVVAVTDQGFANKLISLL  99
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeehhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh......eeee.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------RIBOSOMAL_L7AE    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3v7q B 103 GMEWFPLLGLANRARKVVSGEDLVIKEIRNARAKLVLLTEDASSNTAKKVTDKCNYYKVPYKKVESRAVLGRSIGKEARVVVAVTDQGFANKLISLL 199
                                   112       122       132       142       152       162       172       182       192

Chain C from PDB  Type:PROTEIN  Length:97
 aligned with YLXQ_BACSU | P32729 from UniProtKB/Swiss-Prot  Length:100

    Alignment length:97
                                    12        22        32        42        52        62        72        82        92       
           YLXQ_BACSU     3 GMEWFPLLGLANRARKVVSGEDLVIKEIRNARAKLVLLTEDASSNTAKKVTDKCNYYKVPYKKVESRAVLGRSIGKEARVVVAVTDQGFANKLISLL  99
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeehhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhh...eeee.hhhhhhhhh......eeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------RIBOSOMAL_L7AE    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                 3v7q C 203 GMEWFPLLGLANRARKVVSGEDLVIKEIRNARAKLVLLTEDASSNTAKKVTDKCNYYKVPYKKVESRAVLGRSIGKEARVVVAVTDQGFANKLISLL 299
                                   212       222       232       242       252       262       272       282       292

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 3V7Q)

(no "CATH Domain" information available for 3V7Q)

(no "Pfam Domain" information available for 3V7Q)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (YLXQ_BACSU | P32729)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
	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.
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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3v7e	HOMOLOG YBXF IN SAME PUBLICATION

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