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(-) Description

Title :  CRYSTAL STRUCTURE OF SCHISTOSOME EIF4E COMPLEXED WITH M7GPPPG AND 4E-BP
 
Authors :  W. Liu, R. Zhao, D. N. M. Jones, R. E. Davis
Date :  20 Jun 09  (Deposition) - 25 Aug 09  (Release) - 10 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Protein-Mrna Cap Complex, Acetylation, Phosphoprotein, Protein Synthesis Inhibitor, Translation Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Liu, R. Zhao, C. Mcfarland, J. Kieft, A. Niedzwiecka, M. Jankowska-Anyszka, J. Stepinski, E. Darzynkiewicz, D. N. Jones, R. E. Davis
Structural Insights Into Parasite Eif4E Binding Specificity For M7G And M2, 2, 7G Mrna Cap.
J. Biol. Chem. V. 284 31336 2009
PubMed-ID: 19710013  |  Reference-DOI: 10.1074/JBC.M109.049858
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION 4E
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P-1
    Expression System StrainXA90
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneEIF4E
    Organism ScientificSCHISTOSOMA MANSONI
    Organism Taxid6183
 
Molecule 2 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4E- BINDING PROTEIN 1
    ChainsC
    EngineeredYES
    FragmentRESIDUES 51-67
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEIF4E-BINDING PROTEIN 1, 4E-BP1, PHOSPHORYLATED HEAT- AND ACID-STABLE PROTEIN REGULATED BY INSULIN 1, PHAS- I
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1GTG1Ligand/Ion7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:8 , GLU A:21 , PHE A:22 , PHE A:35 , PHE A:37 , LEU A:41 , ASP A:42 , TRP A:43 , GLY A:75 , ASP A:84 , LYS A:88 , TRP A:89 , GLU A:90 , GLN A:141 , ARG A:143 , LYS A:148 , ARG A:192 , HOH A:208 , HOH A:223 , HOH A:224 , HOH A:238 , HOH A:252 , HOH A:256 , HOH A:276BINDING SITE FOR RESIDUE GTG A 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HXI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3HXI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HXI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HXI)

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003388251ENSE00001381442chr8:37887859-378882363784EBP1_HUMAN1-49490--
1.3ENST000003388253ENSE00001378569chr8:37914599-379147781804EBP1_HUMAN49-109611C:5-1713
1.4ENST000003388254ENSE00002136838chr8:37917422-379178834624EBP1_HUMAN109-118100--

(-) 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:182
                                                                                                                                                                                                                      
               SCOP domains d3hxia_ A: automated matches                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeeeee......hhhh.eeeeeeeeehhhhhhhhhh...........eeeeee........hhhhhh.eeeeee.....hhhhhhhhhhhhhhh....hhhhhhheeeeeee......eeeeee....hhhhhhhhhhhhhhhhh....eeeeehhhhhhh.........eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3hxi A  21 EFPHPLQDSWSYYLFQFRKALDWDECLEKVATFSTIEDFWSVLTHTVRPREITYGKDLYMFKSDIMPKWEDPKNENGGRWLINVTARQDVDFLWDELLMLLIGSDWDTDEEDRQICGAVFQPRSRGSKLSVWLTSDNEEETILSIGRRIKERLELEDTIYFQPVSDQRSQTRGSDCTGKYEI 203
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190    || 201  
                                                                                                                                                                                                        195|      
                                                                                                                                                                                                         197      

Chain C from PDB  Type:PROTEIN  Length:14
 aligned with 4EBP1_HUMAN | Q13541 from UniProtKB/Swiss-Prot  Length:118

    Alignment length:16
                                    57      
          4EBP1_HUMAN    48 GGTRIIYDRKFLMECR  63
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .--....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
           Transcript 1 (1) 1.-------------- Transcript 1 (1)
           Transcript 1 (2) -Exon 1.3        Transcript 1 (2)
                 3hxi C   4 G--RIIYDRKFLMECR  17
                            |  |    11      
                            |  5            
                            4               

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HXI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HXI)

(-) Gene Ontology  (23, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain C   (4EBP1_HUMAN | Q13541)
molecular function
    GO:0008190    eukaryotic initiation factor 4E binding    Interacting selectively and non-covalently with eukaryotic initiation factor 4E, a polypeptide factor involved in the initiation of ribosome-mediated translation.
    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:0051721    protein phosphatase 2A binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 2A.
    GO:0031369    translation initiation factor binding    Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation.
    GO:0030371    translation repressor activity    Antagonizes ribosome-mediated translation of mRNA into a polypeptide.
biological process
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0002192    IRES-dependent translational initiation of linear mRNA    The process where translation initiation recruits the 40S ribosomal subunits via an internal ribosome entry segment (IRES) before an AUG codon is encountered in an appropriate sequence context to initiate linear mRNA translation.
    GO:0031929    TOR signaling    A series of molecular signals mediated by TOR (Target of rapamycin) proteins, members of the phosphoinositide (PI) 3-kinase related kinase (PIKK) family that act as serine/threonine kinases in response to nutrient availability or growth factors.
    GO:0071456    cellular response to hypoxia    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0031333    negative regulation of protein complex assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of protein complex assembly.
    GO:0017148    negative regulation of translation    Any process that stops, prevents, or reduces 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:0045947    negative regulation of translational initiation    Any process that stops, prevents, or reduces the frequency, rate or extent of translational initiation.
    GO:0045931    positive regulation of mitotic cell cycle    Any process that activates or increases the rate or extent of progression through the mitotic 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:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0002931    response to ischemia    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a inadequate blood supply.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.

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 Related Entries

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

UniProtKB/Swiss-Prot
        4EBP1_HUMAN | Q135411ej4 1ejh 1wkw 2jgb 2jgc 2v8w 2v8x 2v8y 3hxg 3m93 3m94 3u7x 4ued 5bxv 5ekv

(-) Related Entries Specified in the PDB File

3hxg CRYSTAL STRUCTURE OF SCHISTSOME EIF4E COMPLEXED WITH M7GPPPA AND 4E-BP