Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF WHEAT C113S MUTANT EIF4E BOUND TO 7-METHYL-GDP
 
Authors :  A. F. Monzingo, A. Dutt-Chaudhuri, J. Sadow, S. Dhaliwal, D. W. Hoffman, J. D. Robertus, K. S. Browning
Date :  15 Sep 06  (Deposition) - 12 Jun 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Eukaryotic Initiation Factor 4E, Eif4E, Cap, Methyl-7-Gdp, Translation Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. F. Monzingo, S. Dhaliwal, A. Dutt-Chaudhuri, A. Lyon, J. H. Sadow, D. W. Hoffman, J. D. Robertus, K. S. Browning
The Structure Of Eukaryotic Translation Initiation Factor-4E From Wheat Reveals A Novel Disulfide Bond.
Plant Physiol. V. 143 1504 2007
PubMed-ID: 17322339  |  Reference-DOI: 10.1104/PP.106.093146
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 39-215
    Mutation: YES
    Organism Common: BREAD WHEAT
    Organism Scientific: TRITICUM AESTIVUM
    Organism Taxid: 4565
    Synonym: EIF4E-1, EIF-4E-1, MRNA CAP-BINDING PROTEIN, EIF- 4F 25 KDA SUBUNIT, EIF-4F P26 SUBUNIT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1M7G1Ligand/Ion7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:58 , TRP A:62 , LYS A:107 , TRP A:108 , GLU A:109 , ARG A:158 , ARG A:163 , HOH A:1012 , HOH A:1066 , HOH A:1076 , HOH A:1092 , HOH A:1093BINDING SITE FOR RESIDUE M7G A 1000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2IDV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IF4EPS00813 Eukaryotic initiation factor 4E signature.IF4E1_WHEAT96-119  1A:96-119

(-) Exons   (0, 0)

(no "Exon" information available for 2IDV)

(-) Sequences/Alignments

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:177
 aligned with IF4E1_WHEAT | P29557 from UniProtKB/Swiss-Prot  Length:215

    Alignment length:177
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       
          IF4E1_WHEAT    39 AHPLENAWTFWFDNPQGKSRQVAWGSTIHPIHTFSTVEDFWGLYNNIHNPSKLNVGADFHCFKNKIEPKWEDPICANGGKWTISCGRGKSDTFWLHTLLAMIGEQFDFGDEICGAVVSVRQKQERVAIWTKNAANEAAQISIGKQWKEFLDYKDSIGFIVHEDAKRSDKGPKNRYTV 215
               SCOP domains d2idva_ A: automated matches                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeee...............eeeeeeeehhhhhhhhhh..hhhhh....eeeeee........hhhhh..eeeeeee....hhhhhhhhhhhhhh....hhh.eeeeeeee....eeeeeee....hhhhhhhhhhhhhhhhh....eeeeehhhhh.........eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------IF4E  PDB: A:96-119     ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2idv A  39 AHPLENAWTFWFDNPQGKSRQVAWGSTIHPIHTFSTVEDFWGLYNNIHNPSKLNVGADFHCFKNKIEPKWEDPISANGGKWTISCGRGKSDTFWLHTLLAMIGEQFDFGDEICGAVVSVRQKQERVAIWTKNAANEAAQISIGKQWKEFLDYKDSIGFIVHEDAKRSDKGPKNRYTV 215
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (IF4E1_WHEAT | P29557)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    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: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.

 Visualization

(-) Interactive Views

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
    M7G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2idv)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2idv
    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
  IF4E1_WHEAT | P29557
    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

(-) Analysis Tools

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
  IF4E1_WHEAT | P29557
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        IF4E1_WHEAT | P29557: 2idr

(-) Related Entries Specified in the PDB File

2idr WILD-TYPE EIF4E