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(-) Description

Title :  COMPLEX CRYSTAL STRUCTURE OF ASCARIS SUUM EIF4E-3 WITH M2,2,7G CAP
 
Authors :  W. Liu, Berkeley Structural Genomics Center (Bsgc)
Date :  19 Mar 10  (Deposition) - 20 Jul 11  (Release) - 14 Dec 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Eif4E, Berkeley Structural Genomics Center, Bsgc, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Liu, M. Jankowska-Anyszka, K. Piecyk, L. Dickson, A. Wallace, A. Niedzwiecka, J. Stepinski, R. Stolarski, E. Darzynkiewicz, J. Kieft, R. Zhao, D. N. Jones, R. E. Davis
Structural Basis For Nematode Eif4E Binding An M2, 2, 7G-Cap And Its Implications For Translation Initiation.
Nucleic Acids Res. V. 39 8820 2011
PubMed-ID: 21965542  |  Reference-DOI: 10.1093/NAR/GKR650

(-) Compounds

Molecule 1 - TRANSLATION INITIATION FACTOR 4E
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30A
    Expression System StrainROSETTA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 49-236
    Organism CommonPIG ROUNDWORM
    Organism ScientificASCARIS SUUM
    Organism Taxid6253
    StrainASCARIS SUUM
 
Molecule 2 - EUKARYOTIC TRANSLATION INITIATION FACTOR 4E-BINDING PROTEIN 1
    ChainsC
    EngineeredYES
    FragmentUNP RESIDUES 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  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2M7M1Ligand/IonN,N,7-TRIMETHYLGUANOSINE 5'-(TRIHYDROGEN DIPHOSPHATE)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:69 , MET A:114 , TRP A:115 , GLU A:116 , ASN A:168 , ARG A:170 , LYS A:175BINDING SITE FOR RESIDUE M7M A 1
2AC2SOFTWARETYR A:60 , LEU A:98 , TYR A:104 , ARG C:1 , ILE C:2BINDING SITE FOR RESIDUE ACE C 0

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M94)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ile A:230 -Pro A:231

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M94)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3M94)

(-) 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:1-014
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:180
 aligned with Q6PKX2_ASCSU | Q6PKX2 from UniProtKB/TrEMBL  Length:236

    Alignment length:185
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227     
         Q6PKX2_ASCSU    48 LRHPLQCHWALWYLKADRSKDWEDCLKQVAVFDTVEDFWSLYNHIQAASGLTWGSDYYLFKEGIKPMWEDENNVKGGRWLVVVDKQKRAQLLDHYWLELLMAIIGEQFEDNGEYICGAVVNVRQKGDKVSLWTRDSLKDDVNLRIGQILKAKLEIPDTEPIRYEVHKDSSVRTGSMVKPRIVIPS 232
               SCOP domains d3m94a_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeeeee......hhhh.eeeeeeeeehhhhhhhhh...hhhhh....eeeeee...............eeeeeee...hhhhhhhhhhhhhhhhhhh..hhhhhh.eeeeeee.....eeeeeee....hhhhhhhhhhhhhhhhh......eeeee..-----........eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m94 A  48 MRHPLQCHWALWYLKADRSKDWEDCLKQVAVFDTVEDFWSLYNHIQAASGLTWGSDYYLFKEGIKPMWEDENNVKGGRWLVVVDKQKRAQLLDHYWLELLMAIIGEQFEDNGEYICGAVVNVRQKGDKVSLWTRDSLKDDVNLRIGQILKAKLEIPDTEPIRYEVHK-----TGSMVKPRIVIPS 232
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207      |  -  |    227     
                                                                                                                                                                                                214   220            

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

    Alignment length:14
                                    60    
          4EBP1_HUMAN    51 RIIYDRKFLMECRN  64
               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 Exon 1.3       Transcript 1
                 3m94 C   1 RIIYDRKFLMECRx   0
                                    10  ||
                                       13|
                                         0-ACE

   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 3M94)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3M94)

(-) Gene Ontology  (27, 28)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6PKX2_ASCSU | Q6PKX2)
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: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.

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 3hxi 3m93 3u7x 4ued 5bxv 5ekv
UniProtKB/TrEMBL
        Q6PKX2_ASCSU | Q6PKX23m93

(-) Related Entries Specified in the PDB File

3m93