1P6V | PR0098 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE TRNA DOMAIN OF TRANSFER-MESSENGER RNA IN COMPLEX WITH SMPB

Authors :   S. Gutmann, P. W. Haebel, L. Metzinger, M. Sutter, B. Felden, N. Ban

Date :   30 Apr 03 (Deposition) - 12 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

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

Keywords :   Smpb, Tmrna, Trans-Translation, Protein-Rna Complex, Rna Binding Protein/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Gutmann, P. W. Haebel, L. Metzinger, M. Sutter, B. Felden, N. Ban
Crystal Structure Of The Transfer-Rna Domain Of Transfer-Messenger Rna In Complex With Smpb
Nature V. 424 699 2003
PubMed-ID: 12904796 | Reference-DOI: 10.1038/NATURE01831
(for further references see the PDB file header)

Molecule 1 - 45-MER
	Chains	:	B, D
	Engineered	:	YES
	Other Details	:	IN VITRO TRANSCRIPTION OF AQUIFEX AEOLICUS TMRNA[DELTA]
	Synthetic	:	YES

Molecule 2 - SSRA-BINDING PROTEIN
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	SMPB
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	63363

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1P6V)

(no "Site" information available for 1P6V)

(no "SS Bond" information available for 1P6V)

(no "Cis Peptide Bond" information available for 1P6V)

(no "SAP(SNP)/Variant" information available for 1P6V)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SSRP	PS01317	SsrA-binding protein.	SSRP_AQUAE	28-40	2	A:27-39 C:27-39

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SSRP	PS01317	SsrA-binding protein.	SSRP_AQUAE	28-40	1	A:27-39 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SSRP	PS01317	SsrA-binding protein.	SSRP_AQUAE	28-40	1	- C:27-39

(no "Exon" information available for 1P6V)

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:125
 aligned with SSRP_AQUAE | O66640 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:128
                                    13        23        33        43        53        63        73        83        93       103       113       123        
           SSRP_AQUAE     4 SDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKL 131
               SCOP domains d1p6va_ A: Small protein B (SmpB)                                                                                                SCOP domains
               CATH domains 1p6vA00 A:3-130  [code=2.40.280.10, no name defined]                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.........eeeeee.....hhhhhhhhhh...ee.....ee......ee...ee......---.......ee...hhhhhhhhhhhhhhhh.eeeeeeeeee...eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SSRP         ------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p6v A   3 SDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHA---NHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKL 130
                                    12        22        32        42        52        62        72   |    82        92       102       112       122        
                                                                                                72  76

Chain B from PDB  Type:RNA  Length:45
                                                                             
                 1p6v B  13 GAUUCGACGGGGACUUCGGUCCUCGGACGCGGGUUCGAUUCCCGC  57
                                    22        32        42        52

Chain C from PDB  Type:PROTEIN  Length:125
 aligned with SSRP_AQUAE | O66640 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:128
                                    13        23        33        43        53        63        73        83        93       103       113       123        
           SSRP_AQUAE     4 SDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHATIENHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKL 131
               SCOP domains d1p6vc_ C: Small protein B (SmpB)                                                                                                SCOP domains
               CATH domains 1p6vC00 C:3-130  [code=2.40.280.10, no name defined]                                                                             CATH domains
           Pfam domains (1) --SmpB-1p6vC01 C:5-72                                                 ---------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --SmpB-1p6vC02 C:5-72                                                 ---------------------------------------------------------- Pfam domains (2)
         Sec.struct. author ...eee...hhhhhh.ee...eee.....hhhhhhhhhhh........eeee....eeee..........---.......ee...hhhhhhhhhhhhhhh.....eeeeeee...eeeeee..ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SSRP         ------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1p6v C   3 SDKIIPIAENKEAKAKYDILETYEAGIVLKGSEVKSLREKGTVSFKDSFVRIENGEAWLYNLYIAPYKHA---NHDPLRKRKLLLHKREIMRLYGKVQEKGYTIIPLKLYWKNNKVKVLIALAKGKKL 130
                                    12        22        32        42        52        62        72   |    82        92       102       112       122        
                                                                                                72  76

Chain D from PDB  Type:RNA  Length:24
                                                        
                 1p6v D  16 UCGACGGGGACUUCGGUCCUCGGA  39
                                    25        35

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Small protein B (SmpB) (7)

Superfamily: Small protein B (SmpB) (7)

Family: Small protein B (SmpB) (7)

Protein domain: Small protein B (SmpB) (7)

Aquifex aeolicus [TaxId: 63363] (2)

1a	d1p6va_	A:
1b	d1p6vc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Small Protein B; Chain: A; (5)

Homologous Superfamily: [code=2.40.280.10, no name defined] (5)

[unclassified] (1)

1a	1p6vA00	A:3-130
1b	1p6vC00	C:3-130

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: SmpB] (2)

Family: SmpB (2)

Aquifex aeolicus (2)

1a	SmpB-1p6vC01	C:5-72
1b	SmpB-1p6vC02	C:5-72

Asymmetric Unit(hide GO term definitions)

Chain A,C (SSRP_AQUAE | O66640)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
biological process
	GO:0070929	trans-translation	A translational elongation process in which transfer of a translating ribosome from one mRNA to another RNA template takes place. Trans-translation occurs during tmRNA release of stalled ribosomes.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1p6v)

	Sites
(no "Sites" information available for 1p6v)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1p6v)

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1p6v
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	SSRP_AQUAE \| O66640
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	SSRP_AQUAE \| O66640
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SSRP_AQUAE \| O66640	:	1k8h 1zc8 2ob7

(no "Related Entries Specified in the PDB File" available for 1P6V)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (3, 3)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File