1UEB - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR P FROM THERMUS THERMOPHILUS HB8

Authors :   K. Hanawa-Suetsugu, S. Sekine, H. Sakai, C. Hori-Takemoto, T. Terada, S. Kuramitsu, M. Shirouzu, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   09 May 03 (Deposition) - 25 May 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Beta Barrel, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Rna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Hanawa-Suetsugu, S. Sekine, H. Sakai, C. Hori-Takemoto, T. Terada, S. Unzai, J. R. H. Tame, S. Kuramitsu, M. Shirouzu, S. Yokoyama
Crystal Structure Of Elongation Factor P From Thermus Thermophilus Hb8
Proc. Natl. Acad. Sci. Usa V. 101 9595 2004
PubMed-ID: 15210970 | Reference-DOI: 10.1073/PNAS.0308667101
(for further references see the PDB file header)

Molecule 1 - ELONGATION FACTOR P
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	EF-P, TT0860

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

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 1UEB)

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EFP	PS01275	Elongation factor P signature.	EFP_THET8	149-168	2	A:149-168 B:349-368

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EFP	PS01275	Elongation factor P signature.	EFP_THET8	149-168	1	A:149-168 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	EFP	PS01275	Elongation factor P signature.	EFP_THET8	149-168	1	- B:349-368

(no "Exon" information available for 1UEB)

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:184
 aligned with EFP_THET8 | Q76G20 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
            EFP_THET8     1 MISVTDLRPGTKVKMDGGLWECVEYQHQKLGRGGAKVVAKFKNLETGATVERTFNSGEKLEDIYVETRELQYLYPEGEEMVFMDLETYEQFAVPRSRVVGAEFFKEGMTALGDMYEGQPIKVTPPTVVELKVVDTPPGVRGDTVSGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGEYVGRA 184
               SCOP domains d1ueba1 A:1-63 Elongation factor P N-terminal domain           d1ueba2 A:64-126                                               d1ueba3 A:127-184                                          SCOP domains
               CATH domains 1uebA01 A:1-63  [code=2.30.30.30, no name defined]             1uebA02 A:64-126 Nucleic acid-binding proteins                 1uebA03 A:127-184 Nucleic acid-binding proteins            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.hhh....eeee..eeeeeeeeeeeee.....eeeeeeee.....eeeeeee...eeee..eeeeeeeeeeee..eeeeee.....eeeee.hhh.hhhhh....eeeeeee..eeeeee...eeeeeeee.............eeeeee....eeeee.......eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------EFP  PDB: A:149-168 ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ueb A   1 MISVTDLRPGTKVKMDGGLWECVEYQHQKLGRGGAKVVAKFKNLETGATVERTFNSGEKLEDIYVETRELQYLYPEGEEMVFMDLETYEQFAVPRSRVVGAEFFKEGMTALGDMYEGQPIKVTPPTVVELKVVDTPPGVRGDTVSGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGEYVGRA 184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180

Chain B from PDB  Type:PROTEIN  Length:178
 aligned with EFP_THET8 | Q76G20 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:184
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180    
            EFP_THET8     1 MISVTDLRPGTKVKMDGGLWECVEYQHQKLGRGGAKVVAKFKNLETGATVERTFNSGEKLEDIYVETRELQYLYPEGEEMVFMDLETYEQFAVPRSRVVGAEFFKEGMTALGDMYEGQPIKVTPPTVVELKVVDTPPGVRGDTVSGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGEYVGRA 184
               SCOP domains d1uebb1 B:201-263 Elongation factor P N-terminal domain        d1uebb2 B:264-326                                              d1uebb3 B:32      7-384                                    SCOP domains
               CATH domains 1uebB01 B:201-263  [code=2.30.30.30, no name defined]          1uebB02 B:264-326 Nucleic acid-binding proteins                1uebB03 B:32      7-384 Nucleic acid-binding proteins      CATH domains
           Pfam domains (1) --EFP_N-1uebB01 B:203-260                                   ------EFP-1uebB03 B:267-320                                 -------Elong-fact-      P_C-1uebB05 B:328-383                  - Pfam domains (1)
           Pfam domains (2) --EFP_N-1uebB02 B:203-260                                   ------EFP-1uebB04 B:267-320                                 -------Elong-fact-      P_C-1uebB06 B:328-383                  - Pfam domains (2)
         Sec.struct. author .ee.hhh....eeee..eeeeeeeeeeeee.....eeeeeeee.....eeeeeee...eeee...eeeeeeeeeee..eeeeee.....eeeehhhhh.hhhhh....eeeeeee..eeeeee...eeeeeeee....------...eeeeee....eeeee.......eeeee....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------EFP  PDB: B:349-368 ---------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ueb B 201 MISVTDLRPGTKVKMDGGLWECVEYQHQKLGRGGAKVVAKFKNLETGATVERTFNSGEKLEDIYVETRELQYLYPEGEEMVFMDLETYEQFAVPRSRVVGAEFFKEGMTALGDMYEGQPIKVTPPTVVELKVVDTPPG------SGGSKPATLETGAVVQVPLFVEPGEVIKVDTRTGEYVGRA 384
                                   210       220       230       240       250       260       270       280       290       300       310       320       330       | -    |  350       360       370       380    
                                                                                                                                                                   338    345

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: Nucleic acid-binding proteins (483)

Thermus thermophilus. Organism_taxid: 274. (5)

1a	1uebA02	A:64-126
1b	1uebB02	B:264-326
1c	1uebA03	A:127-184
1d	1uebB03	B:327-384

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: [code=2.30.30.30, no name defined] (111)

Thermus thermophilus. Organism_taxid: 274. (1)

2a	1uebA01	A:1-63
2b	1uebB01	B:201-263

Asymmetric Unit(hide GO term definitions)

Chain A,B (EFP_THET8 | Q76G20)

molecular function
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0043043	peptide biosynthetic process	The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
	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.
	GO:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
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 1ueb)

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

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

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
	1ueb
		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
	EFP_THET8 \| Q76G20
		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
	EFP_THET8 \| Q76G20
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	EFP_THET8 \| Q76G20	:	4v6a

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

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 (2, 6)

CATH Domains (2, 6)

Pfam Domains (3, 6)

Gene Ontology (5, 5)

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