2UWM - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Title :   C-TERMINAL DOMAIN(WH2-WH4) OF ELONGATION FACTOR SELB IN COMPLEX WITH SECIS RNA

Authors :   T. Ose, N. Soler, L. Rasubala, K. Kuroki, D. Kohda, D. Fourmy, S. Yoshiza K. Maenaka

Date :   22 Mar 07 (Deposition) - 08 May 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.31

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Protein Biosynthesis, Translation, Gtp-Binding, Nucleotide- Binding, Selenocysteine-Specific Elongation Factor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ose, N. Soler, L. Rasubala, K. Kuroki, D. Kohda, D. Fourmy, S. Yoshizawa, K. Maenaka
Structural Basis For Dynamic Interdomain Movement And Rna Recognition Of The Selenocysteine-Specific Elongation Factor Selb.
Structure V. 15 577 2007
PubMed-ID: 17502103 | Reference-DOI: 10.1016/J.STR.2007.03.007

Molecule 1 - SELENOCYSTEINE-SPECIFIC ELONGATION FACTOR
	Atcc	:	39073
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-2T
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	SECIS BINDING DOMAIN, RESIDUES 377-634
	Organism Scientific	:	MOORELLA THERMOACETICA
	Organism Taxid	:	1525
	Synonym	:	SELB TRANSLATION FACTOR

*Molecule 2 - 5'-R(GPGPCPGPUPUPGPCPCPGP GPUPCPUPGPGPCPAPAPCPGPCPC)-3'**
	Chains	:	C, D
	Organism Scientific	:	MOORELLA THERMOACETICA
	Organism Taxid	:	1525
	Synonym	:	MRNA
	Synthetic	:	YES

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2UWM)

(no "Site" information available for 2UWM)

(no "SS Bond" information available for 2UWM)

Asymmetric/Biological Unit

No.	Residues
1	Gln A:441	-	Ala A:442

(no "SAP(SNP)/Variant" information available for 2UWM)

(no "PROSITE Motif" information available for 2UWM)

(no "Exon" information available for 2UWM)

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:193
 aligned with Q2RFK4_MOOTA | Q2RFK4 from UniProtKB/TrEMBL  Length:634

    Alignment length:193
                                   450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630   
         Q2RFK4_MOOTA   441 QAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVG 633
               SCOP domains d2uwma1 A:441-510 C-terminal fragment of elongation factor SelB       d2uwma2 A:511-574 C-terminal fragment of elongation factor SelB d2uwma3 A:575-633                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....eehhhhhhhh....hhhhhhhhhhhhhhh..eee...eeee.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uwm A 441 QAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVG 633
                                   450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630

Chain A from PDB  Type:PROTEIN  Length:193
 aligned with SELB_MOOTH | Q46455 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:193
                                   450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630   
           SELB_MOOTH   441 QAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVG 633
               SCOP domains d2uwma1 A:441-510 C-terminal fragment of elongation factor SelB       d2uwma2 A:511-574 C-terminal fragment of elongation factor SelB d2uwma3 A:575-633                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.....eehhhhhhhh....hhhhhhhhhhhhhhh..eee...eeee.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uwm A 441 QAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVG 633
                                   450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with Q2RFK4_MOOTA | Q2RFK4 from UniProtKB/TrEMBL  Length:634

    Alignment length:203
                                   440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630   
         Q2RFK4_MOOTA   431 DLYAISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVG 633
               SCOP domains ----------d2uwmb1 B:441-510 C-terminal fragment of elongation factor SelB       d2uwmb2 B:511-574 C-terminal fragment of elongation factor SelB d2uwmb3 B:575-633                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhh.....eehhhhhhhhh......hhhhhhhhhhhh..eee...eeee.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uwm B 431 DLYAISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVG 633
                                   440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630

Chain B from PDB  Type:PROTEIN  Length:203
 aligned with SELB_MOOTH | Q46455 from UniProtKB/Swiss-Prot  Length:634

    Alignment length:203
                                   440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630   
           SELB_MOOTH   431 DLYAISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVG 633
               SCOP domains ----------d2uwmb1 B:441-510 C-terminal fragment of elongation factor SelB       d2uwmb2 B:511-574 C-terminal fragment of elongation factor SelB d2uwmb3 B:575-633                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhhhhhhh.....eehhhhhhhhh......hhhhhhhhhhhh..eee...eeee.......hhhhhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhhhhhhhh..eeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uwm B 431 DLYAISTERYQAWWQAVTRALEEFHSRYPLRPGLAREELRSRYFSRLPARVYQALLEEWSREGRLQLAANTVALAGFTPSFSETQKKLLKDLEDKYRVSRWQPPSFKEVAGSFNLDPSELEELLHYLVREGVLVKINDEFYWHRQALGEAREVIKNLASTGPFGLAEARDALGSSRKYVLPLLEYLDQVKFTRRVGDKRVVVG 633
                                   440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630

Chain C from PDB  Type:RNA  Length:23
                                                       
                 2uwm C  13 GGCGUUGCCGGUCUGGCAACGCC  35
                                    22        32

Chain D from PDB  Type:RNA  Length:23
                                                       
                 2uwm D  13 GGCGUUGCCGGUCUGGCAACGCC  35
                                    22        32

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DNA/RNA-binding 3-helical bundle (1299)

Superfamily: Winged helix DNA-binding domain (576)

Family: C-terminal fragment of elongation factor SelB (5)

Protein domain: C-terminal fragment of elongation factor SelB (4)

Moorella thermoacetica [TaxId: 1525] (4)

1a	d2uwma1	A:441-510
1b	d2uwma2	A:511-574
1c	d2uwma3	A:575-633
1d	d2uwmb1	B:441-510
1e	d2uwmb2	B:511-574
1f	d2uwmb3	B:575-633

(no "CATH Domain" information available for 2UWM)

(no "Pfam Domain" information available for 2UWM)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SELB_MOOTH | Q46455)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0001514	selenocysteine incorporation	The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
	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:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B (Q2RFK4_MOOTA | Q2RFK4)

molecular function
	GO:0005525	GTP binding	Interacting selectively and non-covalently with GTP, guanosine triphosphate.
	GO:0003924	GTPase activity	Catalysis of the reaction: GTP + H2O = GDP + phosphate.
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
biological process
	GO:0001514	selenocysteine incorporation	The incorporation of selenocysteine into a peptide; uses a special tRNA that recognizes the UGA codon as selenocysteine, rather than as a termination codon. Selenocysteine is synthesized from serine before its incorporation; it is not a posttranslational modification of peptidyl-cysteine.
	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/Biological 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 2uwm)

	Sites
(no "Sites" information available for 2uwm)

	Cis Peptide Bonds
		Gln A:441 - Ala A:442	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit 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
	2uwm
		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
	Q2RFK4_MOOTA \| Q2RFK4
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL
	SELB_MOOTH \| Q46455
		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
	Q2RFK4_MOOTA \| Q2RFK4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	SELB_MOOTH \| Q46455
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	SELB_MOOTH \| Q46455	:	1lva 1wsu 2ply 2v9v

(no "Related Entries Specified in the PDB File" available for 2UWM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 15)

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