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Title :   STRUCTURAL AND FUNCTIONAL ANALYSIS OF THE E. COLI NUSB-S10 TRANSCRIPTION ANTITERMINATION COMPLEX.

Authors :   X. Luo, M. C. Wahl

Date :   09 May 08 (Deposition) - 13 Jan 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.30

Chains :   Asym./Biol. Unit : A,J

Keywords :   Nusb, S10, Nuse, Nut Site, Phage Lambda, Lambdan Antitermination, Rrn Antitermination, Transcription Control, Rna-Binding, Transcription, Transcription Regulation, Transcription Termination, Ribonucleoprotein, Ribosomal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   X. Luo, H. H. Hsiao, M. Bubunenko, G. Weber, D. L. Court, M. E. Gottesman H. Urlaub, M. C. Wahl
Structural And Functional Analysis Of The E. Coli Nusb-S10 Transcription Antitermination Complex.
Mol. Cell V. 32 791 2008
PubMed-ID: 19111659 | Reference-DOI: 10.1016/J.MOLCEL.2008.10.028

Compounds

Molecule 1 - N UTILIZATION SUBSTANCE PROTEIN B
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETM-11
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NUSB, SSYB, B0416, JW0406
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	PROTEIN NUSB

Molecule 2 - 30S RIBOSOMAL PROTEIN S10
	Chains	:	J
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	RPSJ, NUSE, B3321, JW3283
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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:139
 aligned with NUSB_ECOLI | P0A780 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130         
           NUSB_ECOLI     1 MKPAARRRARECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYLSRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNKK 139
               SCOP domains d3d3ba_ A: automated matches                                                                                                                SCOP domains
               CATH domains 3d3bA00 A:1-139 N-utilizing Substance Protein B Homolog; Chain A                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------D------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d3b A   1 MEPAARRRARECAVQALYSWQLSQNDIADVEYQFLAEQDVKDVDVLYFRELLAGVATNTAYLDGLMKPYLSRLLEELGQVEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVLDKAAPVIRPNKK 139
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain J from PDB  Type:PROTEIN  Length:87
 aligned with RS10_ECOLI | P0A7R5 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:108
                                 1                                                                                                      
                                 |   5        15        25        35        45        55        65        75        85        95        
           RS10_ECOLI     - -----MQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRKERFTVLISPHVNKDARDQYEIRTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG 103
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeee.hhhhhhhhhhhhhhhhhh...eeeeeeeeeee.---------------------.eeeeeeeee..hhhhhhhhhhh.....eeeeeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------RIBOSOMAL_S10   ----------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 3d3b J  -4 GPLGSMQNQRIRIRLKAFDHRLIDQATAEIVETAKRTGAQVRGPIPLPTRS---------------------RTHLRLVDIVEPTEKTVDALMRLDLAAGVDVQISLG  82
                                     5        15        25        35        45|        -         -  |     54        64        74        
                                                                             46                    47

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, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (15, 18)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NUSB_ECOLI | P0A780)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0006353	DNA-templated transcription, termination	The cellular process that completes DNA-templated transcription; the formation of phosphodiester bonds ceases, the RNA-DNA hybrid dissociates, and RNA polymerase releases the DNA.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain J (RS10_ECOLI | P0A7R5)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	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.
	GO:0001072	transcription antitermination factor activity, RNA binding	Binds to RNA, typically within the nascent RNA transcript, to promote readthrough of a transcription termination site and thus extending the length of the RNA transcript produced. Examples of antitermination factors which bind the nascent RNA include the lambda N protein and the HIV-1 tat protein.
biological process
	GO:0031564	transcription antitermination	Regulation of transcription by a mechanism that allows RNA polymerase to continue transcription beyond termination site(s).
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0022627	cytosolic small ribosomal subunit	The small subunit of a ribosome located in the cytosol.
	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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