3R2C - JenaLib

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Biological Unit 2 (Jmol Viewer)

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

Authors :   J. R. Stagno, X. Ji

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

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,J,K,R,S
Biol. Unit 1: A,J,R  (1x)
Biol. Unit 2: B,K,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	:	PDEST42
	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	:	PDEST42
	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
Biological Unit 2 (1x)	:		B		K		S

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 12)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	PEG	10	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 7)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	PEG	6	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (2, 5)

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

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TRP A:18	BINDING SITE FOR RESIDUE PEG A 149
02	AC2	SOFTWARE	GLU A:60 , PHE A:94 , LYS A:96 , HOH A:242	BINDING SITE FOR RESIDUE PEG A 150
03	AC3	SOFTWARE	ILE A:38 , TYR A:44 , ASP B:75	BINDING SITE FOR RESIDUE PEG A 151
04	AC4	SOFTWARE	LYS A:5 , ASP A:109 , LEU A:110 , HOH A:156 , HOH A:194 , HOH A:195 , HOH A:209 , G S:2	BINDING SITE FOR RESIDUE PEG A 152
05	AC5	SOFTWARE	GLU A:27 , LYS A:30 , HOH A:251 , G S:9	BINDING SITE FOR RESIDUE ACT A 153
06	AC6	SOFTWARE	GLU B:60 , ILE B:93 , LYS B:96	BINDING SITE FOR RESIDUE PEG B 149
07	AC7	SOFTWARE	TRP B:18 , GLY B:22 , ARG B:86	BINDING SITE FOR RESIDUE PEG B 150
08	AC8	SOFTWARE	MET B:1 , ARG B:102 , G S:1	BINDING SITE FOR RESIDUE ACT B 151
09	AC9	SOFTWARE	SER A:128 , LYS A:132 , U R:4 , C R:6	BINDING SITE FOR RESIDUE PEG R 13
10	BC1	SOFTWARE	LYS A:112 , HOH A:195 , HOH B:206 , G R:2 , C R:5 , G S:2 , C S:5	BINDING SITE FOR RESIDUE PEG S 13
11	BC2	SOFTWARE	SER B:128 , LYS B:132 , U S:4 , C S:5 , C S:6	BINDING SITE FOR RESIDUE PEG S 14

(no "SS Bond" information available for 3R2C)

Asymmetric Unit

No.	Residues
1	Gly J:38	-	Pro J:39
2	Gly K:38	-	Pro K:39

(no "SAP(SNP)/Variant" information available for 3R2C)

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 3R2C)

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:138
 aligned with NUSB_AQUAE | O66530 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130        
           NUSB_AQUAE     1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3r2c A   1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITSS 138
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with NUSB_AQUAE | O66530 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       
           NUSB_AQUAE     1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITS 137
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----NusB-3r2cB01 B:5-132                                                                                                            ----- Pfam domains (1)
           Pfam domains (2) ----NusB-3r2cB02 B:5-132                                                                                                            ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3r2c B   1 MRYRKGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAKKLVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVDLVKKYADEKAGKFVNGVLSAIYKAYITS 137
                                    10        20        30        40        50        60        70        80        90       100       110       120       130

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

    Alignment length:100
                                    12        22        32        42        52        62        72        82        92       102
           RS10_AQUAE     3 QEKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRKRKWCVLRSPHKFDQSREHFEIREFSRILDIIRFTPQTIEALMEISLPAGVDVEVKM 102
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.--------------.-------eeeeeeeeee.hhhhhhhhhh.......eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------RIBOSOMAL_S10   ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 3r2c J   3 QEKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRK--------------S-------EFSRILDIIRFTPQTIEALMEISLPAGVDVEVKM  81
                                    12        22        32        42   |     -        |-      | 51        61        71        81
                                                                      46             47      48

Chain K from PDB  Type:PROTEIN  Length:80
 aligned with RS10_AQUAE | O66430 from UniProtKB/Swiss-Prot  Length:104

    Alignment length:101
                                    12        22        32        42        52        62        72        82        92       102 
           RS10_AQUAE     3 QEKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRKRKWCVLRSPHKFDQSREHFEIREFSRILDIIRFTPQTIEALMEISLPAGVDVEVKMR 103
               SCOP domains ----------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---Ribosomal_S10-3r2cK01 K:6-81             -------------- -------                                  - Pfam domains (1)
           Pfam domains (2) ---Ribosomal_S10-3r2cK02 K:6-81             -------------- -------                                  - Pfam domains (2)
         Sec.struct. author ...eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee.--------------.-------eeeeeeeeee.hhhhhhhhh........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------RIBOSOMAL_S10   ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------- Transcript
                 3r2c K   3 QEKIRIKLRAYDHRLLDQSVKQIIETVKRTGGVVKGPIPLPTRK--------------S-------EFSRILDIIRFTPQTIEALMEISLPAGVDVEVKMR  82
                                    12        22        32        42   |     -        |-      | 51        61        71        81 
                                                                      46             47      48

Chain R from PDB  Type:DNA/RNA  Length:9
                                         
                 3r2c R   1 GGCUCCUUG   9

Chain S from PDB  Type:RNA  Length:10
                                          
                 3r2c S   1 GGCUCCUUGG  10
                                    10

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 3R2C)

(no "CATH Domain" information available for 3R2C)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: NusB (9)

Aquifex aeolicus (2)

1a	NusB-3r2cB01	B:5-132
1b	NusB-3r2cB02	B:5-132

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

Family: Ribosomal_S10 (20)

Aquifex aeolicus (2)

2a	Ribosomal_S10-3r2cK01	K:6-81
2b	Ribosomal_S10-3r2cK02	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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly J:38 - Pro J:39	[ RasMol ]
		Gly K:38 - Pro K:39	[ RasMol ]

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

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 12)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

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