1RF8 - JenaLib

NMR Structure - model 1 (Jmol Viewer)

NMR Structure - model 1, sites (Jmol Viewer)

NMR Structure - all models (Jmol Viewer)

Title :   SOLUTION STRUCTURE OF THE YEAST TRANSLATION INITIATION FACTOR EIF4E IN COMPLEX WITH M7GDP AND EIF4GI RESIDUES 393 TO 490

Authors :   J. D. Gross, N. J. Moerke, T. Von Der Haar, A. A. Lugovskoy, A. B. Sachs, J. E. G. Mccarthy, G. Wagner

Date :   07 Nov 03 (Deposition) - 23 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   SOLUTION NMR

Resolution :   NOT APPLICABLE

Chains :   NMR Structure  : A,B  (11x)
NMR Structure *: A,B  (1x)

Keywords :   Initiation Factor, Protein Biosynthesis, Translation Regulation, Biosynthetic Protein, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Gross, N. J. Moerke, T. Von Der Haar, A. A. Lugovskoy, A. B. Sachs J. E. Mccarthy, G. Wagner
Ribosome Loading Onto The Mrna Cap Is Driven By Conformational Coupling Between Eif4G And Eif4E.
Cell(Cambridge, Mass. ) V. 115 739 2003
PubMed-ID: 14675538 | Reference-DOI: 10.1016/S0092-8674(03)00975-9

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4E
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21(DE3)
	Expression System Plasmid	:	PET30A
	Expression System Taxid	:	469008
	Gene	:	TIF45, CDC33, YOL139C
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	EIF4E, EIF-4E, MRNA CAP-BINDING PROTEIN, EIF-4F 25 KDA SUBUNIT

Molecule 2 - EUKARYOTIC INITIATION FACTOR 4F SUBUNIT P150
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cell Line	:	BL21
	Expression System Plasmid	:	PGEX-2T
	Expression System Taxid	:	511693
	Fragment	:	RESIDUES 391-488 (SWS:P39935)
	Gene	:	TIF4631, YGR162W
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	EIF4F P150, EIF-4F P150, MRNA CAP-BINDING PROTEIN COMPLEX SUBUNIT P150

		1	2
NMR Structure (11x)	:	A	B
NMR Structure * (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

NMR Structure (2, 5)

No.	Name	Count	Type	Full Name
1	M7G	1	Ligand/Ion	7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
2	MTN	4	Ligand/Ion	S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE

NMR Structure * (2, 5)

No.	Name	Count	Type	Full Name
1	M7G	1	Ligand/Ion	7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE
2	MTN	4	Ligand/Ion	S-[(1-OXYL-2,2,5,5-TETRAMETHYL-2,5-DIHYDRO-1H-PYRROL-3-YL)METHYL] METHANESULFONOTHIOATE

NMR Structure (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:120	BINDING SITE FOR RESIDUE MTN A 320
2	AC2	SOFTWARE	GLU A:128 , CYS A:132 , LEU B:284	BINDING SITE FOR RESIDUE MTN A 321
3	AC3	SOFTWARE	CYS A:169	BINDING SITE FOR RESIDUE MTN A 322
4	AC4	SOFTWARE	CYS A:200 , ASN A:203	BINDING SITE FOR RESIDUE MTN A 323
5	AC5	SOFTWARE	TRP A:58 , ASP A:92 , GLU A:103 , TRP A:104 , GLU A:105 , ARG A:157	BINDING SITE FOR RESIDUE M7G A 325

(no "SS Bond" information available for 1RF8)

(no "Cis Peptide Bond" information available for 1RF8)

(no "SAP(SNP)/Variant" information available for 1RF8)

NMR Structure (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IF4E	PS00813	Eukaryotic initiation factor 4E signature.	IF4E_YEAST	92-115	1	A:92-115

NMR Structure * (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	IF4E	PS00813	Eukaryotic initiation factor 4E signature.	IF4E_YEAST	92-115	1	A:92-115

NMR Structure (2, 2)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YGR162W	1	YGR162W.1	VII:824064-826922	2859	IF4F1_YEAST	1-952	952	1	B:215-314 (gaps)	101

2.1	YOL139C	1	YOL139C.1	XV:61024-60383	642	IF4E_YEAST	1-213	213	1	A:1-213	213

NMR Structure

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:213
 aligned with IF4E_YEAST | P07260 from UniProtKB/Swiss-Prot  Length:213

    Alignment length:213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210   
           IF4E_YEAST     1 MSVEEVSKKFEENVSVDDTTATPKTVLSDSAHFDVKHPLNTKWTLWYTKPAVDKSESWSDLLRPVTSFQTVEEFWAIIQNIPEPHELPLKSDYHVFRNDVRPEWEDEANAKGGKWSFQLRGKGADIDELWLRTLLAVIGETIDEDDSQINGVVLSIRKGGNKFALWTKSEDKEPLLRIGGKFKQVLKLTDDGHLEFFPHSSANGRHPQPSITL 213
               SCOP domains d1rf8a_ A: Translation initiation factor eIF4e                                                                                                                                                                        SCOP domains
               CATH domains 1rf8A00 A:1-213 RNA Cap, Translation Initiation Factor Eif4e                                                                                                                                                          CATH domains
               Pfam domains -------------------------------------IF4E-1rf8A01 A:38-199                                                                                                                                             -------------- Pfam domains
         Sec.struct. author ........................hhhhhh............eeeeee........hhhhhheee.....hhhhhhhhhhhhhhhh.....eeeeee........hhhhhhheeeeeee.....hhhhhhhhhhhhhhhh..........eeeee.....eeeeeee...hhhhhhhhhhhhhhhh........eeeehhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------IF4E  PDB: A:92-115     -------------------------------------------------------------------------------------------------- PROSITE
               Transcript 2 Exon 2.1  PDB: A:1-213 UniProt: 1-213                                                                                                                                                                                 Transcript 2
                 1rf8 A   1 MSVEEVSKKFEENVSVDDTTATPKTVLSDSAHFDVKHPLNTKWTLWYTKPAVDKSESWSDLLRPVTSFQTVEEFWAIIQNIPEPHELPLKSDYHVFRNDVRPEWEDEANAKGGKWSFQLCGKGADIDELWLCTLLAVIGETIDEDDSQINGVVLSIRKGGNKFALWTKCEDKEPLLRIGGKFKQVLKLTDDGHLEFFPHCSANGRHPQPSITL 213
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

Chain B from PDB  Type:PROTEIN  Length:100
 aligned with IF4F1_YEAST | P39935 from UniProtKB/Swiss-Prot  Length:952

    Alignment length:101
                                   397       407       417       427       437       447       457       467       477       487 
          IF4F1_YEAST   388 GTKIGLEAEIETTTDETDDGTNTVSHILNVLKDATPIEDVFSFNYPEGIEGPDIKYKKEHVKYTYGPTFLLQFKDKLNVKADAEWVQSTASKIVIPPGMGR 488
               SCOP domains d1 rf8b_ B: Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------eIF_4G1-1rf8B01 B:223-297                                                  ----------------- Pfam domains
         Sec.struct. author ..-...................hhhhhhhhhhh.....hhhhh...........hhhhh......hhhhhhhhhhhhh....hhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:215-314 (gaps) UniProt: 1-952 [INCOMPLETE]                                           Transcript 1
                 1rf8 B 215 GS-IGLEAEIETTTDETDDGTNTVSHILNVLKDATPIEDVFSFNYPEGIEGPDIKYKKEHVKYTYGPTFLLQFKDKLNVKADAEWVQSTASKIVIPPGMGR 314
                             | |   223       233       243       253       263       273       283       293       303       313 
                           216 |                                                                                                 
                             217

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 '\|'

NMR Structure

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: RNA Cap, Translation Initiation Factor Eif4e (11)

Homologous Superfamily: RNA Cap, Translation Initiation Factor Eif4e (11)

Baker's yeast (Saccharomyces cerevisiae) (2)

1rf8A00

A:1-213

NMR Structure(hide GO term definitions)

Chain A (IF4E_YEAST | P07260)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0032266	phosphatidylinositol-3-phosphate binding	Interacting selectively and non-covalently with phosphatidylinositol-3-phosphate, a derivative of phosphatidylinositol in which the inositol ring is phosphorylated at the 3' position.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
	GO:0051726	regulation of cell cycle	Any process that modulates the rate or extent of progression through the cell cycle.
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	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:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	GO:0016281	eukaryotic translation initiation factor 4F complex	The eukaryotic translation initiation factor 4F complex is composed of eIF4E, eIF4A and eIF4G; it is involved in the recognition of the mRNA cap, ATP-dependent unwinding of the 5'-terminal secondary structure and recruitment of the mRNA to the ribosome.
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
	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.

Chain B (IF4F1_YEAST | P39935)

molecular function
	GO:0003723	RNA binding	Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
biological process
	GO:0006417	regulation of translation	Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
	GO:0042273	ribosomal large subunit biogenesis	A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a large ribosomal subunit; includes transport to the sites of protein synthesis.
	GO:0034063	stress granule assembly	The aggregation, arrangement and bonding together of proteins and RNA molecules to form a stress granule.
	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:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
cellular component
	GO:0000932	P-body	A focus in the cytoplasm where mRNAs may become inactivated by decapping or some other mechanism. Protein and RNA localized to these foci are involved in mRNA degradation, nonsense-mediated mRNA decay (NMD), translational repression, and RNA-mediated gene silencing.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0010494	cytoplasmic stress granule	A dense aggregation in the cytosol composed of proteins and RNAs that appear when the cell is under stress.
	GO:0016281	eukaryotic translation initiation factor 4F complex	The eukaryotic translation initiation factor 4F complex is composed of eIF4E, eIF4A and eIF4G; it is involved in the recognition of the mRNA cap, ATP-dependent unwinding of the 5'-terminal secondary structure and recruitment of the mRNA to the ribosome.

NMR Structure
	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
		M7G	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MTN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1rf8)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ NMR Structure - model 1 PNG format \| NMR Structure - model 1, sites PNG format \| NMR Structure - all models 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
	1rf8
		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
	IF4E_YEAST \| P07260
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	IF4F1_YEAST \| P39935
		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
	IF4E_YEAST \| P07260
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	IF4F1_YEAST \| P39935
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	IF4E_YEAST \| P07260	:	1ap8
	IF4F1_YEAST \| P39935	:	2vso 2vsx

1ap8	YEAST TRANSLATION INITATION FACTOR EIF4E IN COMPLEX WITH M7GDP

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (2, 2)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (1, 1)

Pfam Domains (2, 2)

Gene Ontology (17, 26)

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