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(-) Description

Title :  STRUCTURE OF EUKARYOTIC TRANSLATION INITIATION FACTOR EIF3I COMPLEX WITH EIF3B C-TERMINUS (655-700)
 
Authors :  D. Daujotyte, P. J. Lukavsky
Date :  01 Aug 11  (Deposition) - 05 Oct 11  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  B,D,E,F
Biol. Unit 1:  B,E  (1x)
Biol. Unit 2:  D,F  (1x)
Keywords :  Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Herrmannova, D. Daujotyte, J. C. Yang, L. Cuchalova, F. Gorrec, S. Wagner, I. Danyi, P. J. Lukavsky, L. Shivaya Valasek
Structural Analysis Of An Eif3 Subcomplex Reveals Conserved Interactions Required For A Stable And Proper Translation Pre-Initiation Complex Assembly.
Nucleic Acids Res. V. 40 2294 2012
PubMed-ID: 22090426  |  Reference-DOI: 10.1093/NAR/GKR765

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: EIF3I, EUKARYOTIC TRANSLATION INITIATION FACTOR 3 39 KDA SUBUNIT, EIF-3 39 KDA SUBUNIT, EIF3 P39, TIF34
 
Molecule 2 - EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
    Chains: E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 693-739
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: EIF3B, CELL CYCLE REGULATION AND TRANSLATION INITIATION PROTEIN, EUKARYOTIC TRANSLATION INITIATION FACTOR 3 90 KDA SUBUNIT, EIF3 P90, TRANSLATION INITIATION FACTOR EIF3 P90 SUBUNIT, PRT1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : BDEF
Biological Unit 1 (1x): B E 
Biological Unit 2 (1x):  D F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3ZWL)

(-) Sites  (0, 0)

(no "Site" information available for 3ZWL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.EIF3I_YEAST67-81
 		  2B:67-81
D:67-81
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.EIF3I_YEAST67-81
 		  1B:67-81
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1WD_REPEATS_1PS00678 Trp-Asp (WD) repeats signature.EIF3I_YEAST67-81
 		  1-
D:67-81

(-) Exons   (0, 0)

(no "Exon" information available for 3ZWL)

(-) Sequences/Alignments

Asymmetric 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 B from PDB  Type:PROTEIN  Length:339
 aligned with EIF3I_YEAST | P40217 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:352
                                      1                                                                                                                                                                                                                                                                                                                                                     
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  
          EIF3I_YEAST     - ----------MKAIKLTGHERPLTQVKYNKEGDLLFSCSKDSSASVWYSLNGERLGTLDGHTGTIWSIDVDCFTKYCVTGSADYSIKLWDVSNGQCVATWKSPVPVKRVEFSPCGNYFLAILDNVMKNPGSINIYEIERDSATHELTKVSEEPIHKIITHEGLDAATVAGWSTKGKYIIAGHKDGKISKYDVSNNYEYVDSIDLHEKSISDMQFSPDLTYFITSSRDTNSFLVDVSTLQVLKKYETDCPLNTAVITPLKEFIILGGGQEAKDVTTTSANEGKFEARFYHKIFEEEIGRVQGHFGPLNTVAISPQGTSYASGGEDGFIRLHHFEKSYFDFKYDVEKAAEAKEH 342
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeee.....eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee...eeeeee.....eeeeee....eeeeee.....eeeeee........eeeeeeeee......eeee.....eeee.......eeeeee.hhh.eeeeee...eeeeee.....eeeeeee.....eeeeee.....eeeeee...eeeeee.....eeeeee....eeeeee.....eeeeee...-------------.eeeeee.....eeeeee.....eeeeee.....eeeeee...eeeeeeehhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------WD_REPEATS_1   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zwl B  -9 GENLYFQGSHMKAIKLTGHERPLTQVKYNKEGDLLFSCSKDSSASVWYSLNGERLGTLDGHTGTIWSIDVDCFTKYCVTGSADYSIKLWDVSNGQCVATWKSPVPVKRVEFSPCGNYFLAILDNVMKNPGSINIYEIERDSATHELTKVSEEPIHKIITHEGLDAATVAGWSTKGKYIIAGHKDGKISKYDVSNNYEYVDSIDLHEKSISDMQFSPDLTYFITSSRDTNSFLVDVSTLQVLKKYETDCPLNTAVITPLKEFIILGGGQE-------------FEARFYHKIFEEEIGRVQGHFGPLNTVAISPQGTSYASGGEDGFIRLHHFEKSYFDFKYDVEKAAEAKEH 342
                                     0        10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250        |-         -  |    280       290       300       310       320       330       340  
                                                                                                                                                                                                                                                                                                      259           273                                                                     


Chain D from PDB  Type:PROTEIN  Length:352
 aligned with EIF3I_YEAST | P40217 from UniProtKB/Swiss-Prot  Length:347

    Alignment length:352
                                      1                                                                                                                                                                                                                                                                                                                                                     
                                     -|       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  
          EIF3I_YEAST     - ----------MKAIKLTGHERPLTQVKYNKEGDLLFSCSKDSSASVWYSLNGERLGTLDGHTGTIWSIDVDCFTKYCVTGSADYSIKLWDVSNGQCVATWKSPVPVKRVEFSPCGNYFLAILDNVMKNPGSINIYEIERDSATHELTKVSEEPIHKIITHEGLDAATVAGWSTKGKYIIAGHKDGKISKYDVSNNYEYVDSIDLHEKSISDMQFSPDLTYFITSSRDTNSFLVDVSTLQVLKKYETDCPLNTAVITPLKEFIILGGGQEAKDVTTTSANEGKFEARFYHKIFEEEIGRVQGHFGPLNTVAISPQGTSYASGGEDGFIRLHHFEKSYFDFKYDVEKAAEAKEH 342
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee...eeeeee.....eeeeee....eeeeee.....eeeeee........eeeeeeeee......eeee.....eeee.......eeeeee.hhh.eeeeee...eeeeee.....eeeeeee.....eeeeee.....eeeeee...eeeeee.....eeeeee....eeeeee.....eeeeee................eeeeeee.....eeeeeeee...eeeeee.....eeeeee....eeeeeehhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------WD_REPEATS_1   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3zwl D  -9 GENLYFQGSHMKAIKLTGHERPLTQVKYNKEGDLLFSCSKDSSASVWYSLNGERLGTLDGHTGTIWSIDVDCFTKYCVTGSADYSIKLWDVSNGQCVATWKSPVPVKRVEFSPCGNYFLAILDNVMKNPGSINIYEIERDSATHELTKVSEEPIHKIITHEGLDAATVAGWSTKGKYIIAGHKDGKISKYDVSNNYEYVDSIDLHEKSISDMQFSPDLTYFITSSRDTNSFLVDVSTLQVLKKYETDCPLNTAVITPLKEFIILGGGQEAKDVTTTSANEGKFEARFYHKIFEEEIGRVQGHFGPLNTVAISPQGTSYASGGEDGFIRLHHFEKSYFDFKYDVEKAAEAKEH 342
                                     0        10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340  


Chain E from PDB  Type:PROTEIN  Length:39
 aligned with EIF3B_YEAST | P06103 from UniProtKB/Swiss-Prot  Length:763

    Alignment length:39
                                   709       719       729         
          EIF3B_YEAST   700 RDLILHQRELLKQWTEYREKIGQEMEKSMNFKIFDVQPE 738
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 3zwl E 661 RDLILHQRELLKQWTEYREKIGQEMEKSMNFKIFDVQPE 699
                                   670       680       690         


Chain F from PDB  Type:PROTEIN  Length:39
 aligned with EIF3B_YEAST | P06103 from UniProtKB/Swiss-Prot  Length:763

    Alignment length:39
                                   709       719       729         
          EIF3B_YEAST   700 RDLILHQRELLKQWTEYREKIGQEMEKSMNFKIFDVQPE 738
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 3zwl F 661 RDLILHQRELLKQWTEYREKIGQEMEKSMNFKIFDVQPE 699
                                   670       680       690
   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  (0, 0)

(no "SCOP Domain" information available for 3ZWL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 30)

Asymmetric Unit(hide GO term definitions)
Chain B,D   (EIF3I_YEAST | P40217)
molecular function
    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:0002183    cytoplasmic translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein in the cytoplasm. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
    GO:0001731    formation of translation preinitiation complex    The joining of the small ribosomal subunit, ternary complex, and mRNA.
    GO:0006446    regulation of translational initiation    Any process that modulates the frequency, rate or extent of translational initiation.
    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:0002188    translation reinitiation    A gene-specific translational control mechanism where the small ribosomal subunit remains attached to the mRNA following termination of translation, then resumes scanning on the same mRNA molecule and initiates again at a downstream start site. Reinitiation depends on de novo recruitment of the ternary complex that is required to recognize the next AUG codon.
    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:0016282    eukaryotic 43S preinitiation complex    A protein complex composed of the 40S ribosomal subunit plus eIF1A, eIF3, and eIF2-GTP-bound methionyl-initiator methionine tRNA.
    GO:0033290    eukaryotic 48S preinitiation complex    A protein complex composed of the small ribosomal subunit, eIF3, eIF1A, methionyl-initiatior methionine and a capped mRNA. The complex is initially positioned at the 5'-end of the capped mRNA.
    GO:0005852    eukaryotic translation initiation factor 3 complex    A complex of several polypeptides that plays at least two important roles in protein synthesis: First, eIF3 binds to the 40S ribosome and facilitates loading of the Met-tRNA/eIF2.GTP ternary complex to form the 43S preinitiation complex. Subsequently, eIF3 apparently assists eIF4 in recruiting mRNAs to the 43S complex. The eIF3 complex contains five conserved core subunits, and may contain several additional proteins; the non-core subunits are thought to mediate association of the complex with specific sets of mRNAs.
    GO:0043614    multi-eIF complex    A multifactor complex composed of multiple translation initiation factors and the initiatior tRNAiMet, which is ready to bind to the small (40S) ribosome to form the 43S preinitiation complex. In S. cerevisiae, this complex is composed of eIF1, eIF2, eIF3, and eIF5.

Chain E,F   (EIF3B_YEAST | P06103)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    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: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.
    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.
biological process
    GO:0002183    cytoplasmic translational initiation    The process preceding formation of the peptide bond between the first two amino acids of a protein in the cytoplasm. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.
    GO:0001731    formation of translation preinitiation complex    The joining of the small ribosomal subunit, ternary complex, and mRNA.
    GO:0006446    regulation of translational initiation    Any process that modulates the frequency, rate or extent of translational initiation.
    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:0016282    eukaryotic 43S preinitiation complex    A protein complex composed of the 40S ribosomal subunit plus eIF1A, eIF3, and eIF2-GTP-bound methionyl-initiator methionine tRNA.
    GO:0033290    eukaryotic 48S preinitiation complex    A protein complex composed of the small ribosomal subunit, eIF3, eIF1A, methionyl-initiatior methionine and a capped mRNA. The complex is initially positioned at the 5'-end of the capped mRNA.
    GO:0005852    eukaryotic translation initiation factor 3 complex    A complex of several polypeptides that plays at least two important roles in protein synthesis: First, eIF3 binds to the 40S ribosome and facilitates loading of the Met-tRNA/eIF2.GTP ternary complex to form the 43S preinitiation complex. Subsequently, eIF3 apparently assists eIF4 in recruiting mRNAs to the 43S complex. The eIF3 complex contains five conserved core subunits, and may contain several additional proteins; the non-core subunits are thought to mediate association of the complex with specific sets of mRNAs.
    GO:0043614    multi-eIF complex    A multifactor complex composed of multiple translation initiation factors and the initiatior tRNAiMet, which is ready to bind to the small (40S) ribosome to form the 43S preinitiation complex. In S. cerevisiae, this complex is composed of eIF1, eIF2, eIF3, and eIF5.

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  3zwl
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  EIF3I_YEAST | P40217
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 Related Entries

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

UniProtKB/Swiss-Prot
        EIF3B_YEAST | P06103: 3jap 3jaq 3ns5 3ns6 4u1e 4u1f
        EIF3I_YEAST | P40217: 3jap 3jaq 5a5u

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3ZWL)