3R2D - JenaLib

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Title :   CRYSTAL STRUCTURE OF ANTITERMINATION FACTORS NUSB AND NUSE IN COMPLEX WITH DSRNA

Authors :   J. R. Stagno, X. Ji

Date :   14 Mar 11 (Deposition) - 22 Jun 11 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym. Unit : A,B,J,K,R,S
Biol. Unit 1: A,J,R,S  (1x)
Biol. Unit 2: B,K,R,S  (1x)

Keywords :   Cross Species Nusb-Nuse-Rna Interaction, Transcription Elongation, Gene Regulation, Protein-Rna Interaction, Transcription-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Stagno, A. S. Altieri, M. Bubunenko, S. G. Tarasov, J. Li, D. L. Court, R. A. Byrd, X. Ji
Structural Basis For Rna Recognition By Nusb And Nuse In Th Initiation Of Transcription Antitermination.
Nucleic Acids Res. V. 39 7803 2011
PubMed-ID: 21652641 | Reference-DOI: 10.1093/NAR/GKR418

Molecule 1 - N UTILIZATION SUBSTANCE PROTEIN B
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST527
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	AQ_133, NUSB
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	PROTEIN NUSB

Molecule 2 - 30S RIBOSOMAL PROTEIN S10
	Chains	:	J, K
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST527
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	SEE REMARK 999
	Gene	:	AQ_008, NUSE, RPSJ
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Synonym	:	PROTEIN NUSE

*Molecule 3 - 5'-R(GPGPCPUPCPCPUPUPGPGPCPA)-3'*
	Chains	:	R, S
	Engineered	:	YES
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363
	Other Details	:	BOXA RNA
	Synthetic	:	YES

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	J	K	R	S
Biological Unit 1 (1x)	:	A		J		R	S
Biological Unit 2 (1x)	:		B		K	R	S

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	PEG	5	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	PEG	4	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP B:18 , ASP B:19	BINDING SITE FOR RESIDUE PEG B 149
2	AC2	SOFTWARE	HIS B:57 , PHE B:94 , ARG K:11 , ARG K:45	BINDING SITE FOR RESIDUE PEG B 150
3	AC3	SOFTWARE	GLY B:101 , ILE B:105	BINDING SITE FOR RESIDUE PEG B 151
4	AC4	SOFTWARE	TYR B:44	BINDING SITE FOR RESIDUE PEG B 152

(no "SS Bond" information available for 3R2D)

Asymmetric Unit

No.	Residues
1	Met A:0	-	Met A:1
2	Gly J:38	-	Pro J:39
3	Gly K:38	-	Pro K:39

(no "SAP(SNP)/Variant" information available for 3R2D)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S10	PS00361	Ribosomal protein S10 signature.	RS10_AQUAE	29-44	2	J:29-44 K:29-44

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S10	PS00361	Ribosomal protein S10 signature.	RS10_AQUAE	29-44	1	J:29-44 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RIBOSOMAL_S10	PS00361	Ribosomal protein S10 signature.	RS10_AQUAE	29-44	1	- K:29-44

(no "Exon" information available for 3R2D)

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:132
 aligned with NUSB_AQUAE | O66530 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:135
                             1                                                                                                                                     
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129     
           NUSB_AQUAE     - -MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAY 134
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2d A   0 MMRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHL---SIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAY 134
                                     9        19        29        39        49        59        69   |    79        89        99       109       119       129     
                                                                                                69  73

Chain B from PDB  Type:PROTEIN  Length:138
 aligned with NUSB_AQUAE | O66530 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:138
                             1                                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129        
           NUSB_AQUAE     - -MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITS 137
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----NusB-3r2dB01 B:5-132                                                                                                            ----- Pfam domains (1)
           Pfam domains (2) -----NusB-3r2dB02 B:5-132                                                                                                            ----- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r2d B   0 MMRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITS 137
                                     9        19        29        39        49        59        69        79        89        99       109       119       129

Chain J from PDB  Type:PROTEIN  Length:79
 aligned with RS10_AQUAE | O66430 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:100
                                    13        23        33        43        53        63        73        83        93       103
           RS10_AQUAE     4 EKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRKRKWCVLRSPHKFDQSREHFEIREFSRILDIIRFTPQTIEALMEISLPAGVDVEVKMR 103
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.--------------.-------eeeeeeeeee.hhhhhhhhhhh......eeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------RIBOSOMAL_S10   ----------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3r2d J   4 EKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRK--------------S-------EFSRILDIIRFTPQTIEALMEISLPAGVDVEVKMR  82
                                    13        23        33        43  |      -       | -     |  52        62        72        82
                                                                     46             47      48

Chain K from PDB  Type:PROTEIN  Length:79
 aligned with RS10_AQUAE | O66430 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:100
                                    13        23        33        43        53        63        73        83        93       103
           RS10_AQUAE     4 EKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRKRKWCVLRSPHKFDQSREHFEIREFSRILDIIRFTPQTIEALMEISLPAGVDVEVKMR 103
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Ribosomal_S10-3r2dK01 K:6-81             -------------- -------                                  - Pfam domains (1)
           Pfam domains (2) --Ribosomal_S10-3r2dK02 K:6-81             -------------- -------                                  - Pfam domains (2)
         Sec.struct. author ..eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.--------------.-------eeeeeeeeee.hhhhhhhhhhh......eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------RIBOSOMAL_S10   ----------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3r2d K   4 EKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRK--------------S-------EFSRILDIIRFTPQTIEALMEISLPAGVDVEVKMR  82
                                    13        23        33        43  |      -       | -     |  52        62        72        82
                                                                     46             47      48

Chain R from PDB  Type:RNA  Length:12
                                            
                 3r2d R   1 GGCUCCUUGGCA  12
                                    10

Chain S from PDB  Type:RNA  Length:8
                                        
                 3r2d S   5 CCUUGGCA  12

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 3R2D)

(no "CATH Domain" information available for 3R2D)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: NusB] (9)

Family: NusB (9)

Aquifex aeolicus (2)

1a	NusB-3r2dB01	B:5-132
1b	NusB-3r2dB02	B:5-132

Clan: no clan defined [family: Ribosomal_S10] (20)

Family: Ribosomal_S10 (20)

Aquifex aeolicus (2)

2a	Ribosomal_S10-3r2dK01	K:6-81
2b	Ribosomal_S10-3r2dK02	K:6-81

Asymmetric Unit(hide GO term definitions)

Chain A,B (NUSB_AQUAE | O66530)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
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.

Chain J,K (RS10_AQUAE | O66430)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	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.
	GO:0015935	small ribosomal subunit	The smaller of the two subunits of a ribosome.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly J:38 - Pro J:39	[ RasMol ]
		Gly K:38 - Pro K:39	[ RasMol ]
		Met A:0 - Met A:1	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3r2d
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UniProtKB/Swiss-Prot
	NUSB_AQUAE \| O66530	:	2jr0 3r2c 4eya
	RS10_AQUAE \| O66430	:	3r2c

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

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