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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF EUKARYOTIC TRANSLATION INITIATION FACTOR 5B AND 1A COMPLEX
 
Authors :  A. Zheng, R. Yamamoto, T. Ose, J. Yu, I. Tanaka, M. Yao
Date :  20 May 13  (Deposition) - 19 Nov 14  (Release) - 04 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Flexible, Eukaryotic Translation Initiation, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Zheng, J. Yu, R. Yamamoto, T. Ose, I. Tanaka, M. Yao
X-Ray Structures Of Eif5B And The Eif5B-Eif1A Complex: The Conformational Flexibility Of Eif5B Is Restricted On The Ribosome By Interaction With Eif1A
Acta Crystallogr. , Sect. D V. 70 3090 2014
PubMed-ID: 25478828  |  Reference-DOI: 10.1107/S1399004714021476

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 5B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 401-1002
    Gene: FUN12, YAL035W
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: EIF-5B, TRANSLATION INITIATION FACTOR IF-2
 
Molecule 2 - EUKARYOTIC TRANSLATION INITIATION FACTOR 1A
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: B834-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 27-153
    Gene: TIF11, YMR260C, YM8156.02C
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: EIF-1A, EUKARYOTIC TRANSLATION INITIATION FACTOR 4C, EIF-4C

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (1x):  B 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3WBK)

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:9 -A:94
2B:9 -B:94

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:478 -Pro A:479
2Leu B:284 -Arg B:285
3Glu C:120 -Glu C:121

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WBK)

(-) 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 A from PDB  Type:PROTEIN  Length:590
 aligned with IF2P_YEAST | P39730 from UniProtKB/Swiss-Prot  Length:1002

    Alignment length:601
                                   411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001 
          IF2P_YEAST    402 DLRSPICCILGHVDTGKTKLLDKIRQTNVQGGEAGGITQQIGATYFPIDAIKAKTKVMAEYEKQTFDVPGLLVIDTPGHESFSNLRSRGSSLCNIAILVIDIMHGLEQQTIESIKLLRDRKAPFVVALNKIDRLYDWKAIPNNSFRDSFAKQSRAVQEEFQSRYSKIQLELAEQGLNSELYFQNKNMSKYVSIVPTSAVTGEGVPDLLWLLLELTQKRMSKQLMYLSHVEATILEVKVVEGFGTTIDVILSNGYLREGDRIVLCGMNGPIVTNIRALLTPQPLRELRLKSEYVHHKEVKAALGVKIAANDLEKAVSGSRLLVVGPEDDEDELMDDVMDDLTGLLDSVDTTGKGVVVQASTLGSLEALLDFLKDMKIPVMSIGLGPVYKRDVMKASTMLEKAPEYAVMLCFDVKVDKEAEQYAEQEGIKIFNADVIYHLFDSFTAYQEKLLEERRKDFLDYAIFPCVLQTLQIINKRGPMIIGVDVLEGTLRVGTPICAVKTDPTTKERQTLILGKVISLEINHQPVQEVKKGQTAAGVAVRLEDPSGQQPIWGRHVDENDTLYSLVSRRSIDTLKDKAFRDQVARSDWLLLKKLKVVFGIE 1002
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhhhhhhhh..-----..........eeeehhhhhhhhhhhhhh........eeeee..hhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhhhhhh..eeeeeehhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee.hhh......eeeee.......hhhhhhhhhhhhhh...------....eeeeeeeeee...eeeeeeeeee..ee...eeeeee..eeeeee..eeee.............ee..ee...eeeeee...........eeee.....hhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh....hhhh.eeeee....hhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee.....eeeeeeeeeeee...eeee............eeeeeeeeeee..eee.eee.......eeeeee..................eee..hhhhhhhhhh.......hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3wbk A    2 DLRSPICCILGHVDTGKTKLLDKIRQTN-----AGGITQQIGATYFPIDAIKAKTKVMAEYEKQTFDVPGLLVIDTPGHESFSNLRSRGSSLCNIAILVIDIMHGLEQQTIESIKLLRDRKAPFVVALNKIDRLYDWKAIPNNSFRDSFAKQSRAVQEEFQSRYSKIQLELAEQGLNSELYFQNKNMSKYVSIVPTSAVTGEGVPDLLWLLLELTQKRM------LSHVEATILEVKVVEGFGTTIDVILSNGYLREGDRIVLCGMNGPIVTNIRALLTPQPLRELRLKSEYVHHKEVKAALGVKIAANDLEKAVSGSRLLVVGPEDDEDELMDDVMDDLTGLLDSVDTTGKGVVVQASTLGSLEALLDFLKDMKIPVMSIGLGPVYKRDVMKASTMLEKAPEYAVMLCFDVKVDKEAEQYAEQEGIKIFNADVIYHLFDSFTAYQEKLLEERRKDFLDYAIFPCVLQTLQIINKRGPMIIGVDVLEGTLRVGTPICAVKTDPTTKERQTLILGKVISLEINHQPVQEVKKGQTAAGVAVRLEDPSGQQPIWGRHVDENDTLYSLVSRRSIDTLKDKAFRDQVARSDWLLLKKLKVVFGIE  602
                                    11        21       | -   |    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        |-     | 231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601 
                                                      29    35                                                                                                                                                                                      220    227                                                                                                                                                                                                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:590
 aligned with IF2P_YEAST | P39730 from UniProtKB/Swiss-Prot  Length:1002

    Alignment length:601
                                   411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831       841       851       861       871       881       891       901       911       921       931       941       951       961       971       981       991      1001 
          IF2P_YEAST    402 DLRSPICCILGHVDTGKTKLLDKIRQTNVQGGEAGGITQQIGATYFPIDAIKAKTKVMAEYEKQTFDVPGLLVIDTPGHESFSNLRSRGSSLCNIAILVIDIMHGLEQQTIESIKLLRDRKAPFVVALNKIDRLYDWKAIPNNSFRDSFAKQSRAVQEEFQSRYSKIQLELAEQGLNSELYFQNKNMSKYVSIVPTSAVTGEGVPDLLWLLLELTQKRMSKQLMYLSHVEATILEVKVVEGFGTTIDVILSNGYLREGDRIVLCGMNGPIVTNIRALLTPQPLRELRLKSEYVHHKEVKAALGVKIAANDLEKAVSGSRLLVVGPEDDEDELMDDVMDDLTGLLDSVDTTGKGVVVQASTLGSLEALLDFLKDMKIPVMSIGLGPVYKRDVMKASTMLEKAPEYAVMLCFDVKVDKEAEQYAEQEGIKIFNADVIYHLFDSFTAYQEKLLEERRKDFLDYAIFPCVLQTLQIINKRGPMIIGVDVLEGTLRVGTPICAVKTDPTTKERQTLILGKVISLEINHQPVQEVKKGQTAAGVAVRLEDPSGQQPIWGRHVDENDTLYSLVSRRSIDTLKDKAFRDQVARSDWLLLKKLKVVFGIE 1002
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.hhhhhhhhhhhhhhh.--------..ee....eeeehhhhhhhhhhhhhh........eeeee.....hhhhhhh........eeeeeee.....hhhhhhhhhhhhhhh..eeeeeehhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee.hhh......eeeee.......hhhhhhhhhhhhhh..hhhhhh.....eeeeeeeeee...eeeeeeeeee.eee...eeee......eeee..eeeee....---....eee..eee...eeeee...........eeee.....hhhhhhhhhhhhhhhhhh........eeee..hhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhh....eeee.....hhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeeee....eeeeeeeeeeeee...eeeeeeee....eeeeeeeeeeeeeee..eee.eee.......eeeeee..................eee..hhhhhhhh.hhhhhh..hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3wbk B    2 DLRSPICCILGHVDTGKTKLLDKIRQT--------GITQQIGATYFPIDAIKAKTKVMAEYEKQTFDVPGLLVIDTPGHESFSNLRSRGSSLCNIAILVIDIMHGLEQQTIESIKLLRDRKAPFVVALNKIDRLYDWKAIPNNSFRDSFAKQSRAVQEEFQSRYSKIQLELAEQGLNSELYFQNKNMSKYVSIVPTSAVTGEGVPDLLWLLLELTQKRMSKQLMYLSHVEATILEVKVVEGFGTTIDVILSNGYLREGDRIVLCGMNGPIVTNIRALLTPQPLR---LKSEYVHHKEVKAALGVKIAANDLEKAVSGSRLLVVGPEDDEDELMDDVMDDLTGLLDSVDTTGKGVVVQASTLGSLEALLDFLKDMKIPVMSIGLGPVYKRDVMKASTMLEKAPEYAVMLCFDVKVDKEAEQYAEQEGIKIFNADVIYHLFDSFTAYQEKLLEERRKDFLDYAIFPCVLQTLQIINKRGPMIIGVDVLEGTLRVGTPICAVKTDPTTKERQTLILGKVISLEINHQPVQEVKKGQTAAGVAVRLEDPSGQQPIWGRHVDENDTLYSLVSRRSIDTLKDKAFRDQVARSDWLLLKKLKVVFGIE  602
                                    11        21      |  -     |  41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281   |   291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601 
                                                     28       37                                                                                                                                                                                                                                                     285 289                                                                                                                                                                                                                                                                                                                         


Chain C from PDB  Type:PROTEIN  Length:11
 aligned with IF1A_YEAST | P38912 from UniProtKB/Swiss-Prot  Length:153

    Alignment length:11
                                   152 
          IF1A_YEAST    143 GEDEELDIDDI  153
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                3wbk C  117 GEDEELDIDDI  127
                                   126
   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 3WBK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (22, 28)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IF2P_YEAST | P39730)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    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:0001732    formation of cytoplasmic translation initiation complex    Joining of the large subunit, with release of IF2/eIF2 and IF3/eIF3. This leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site.
    GO:0000462    maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)    Any process involved in the maturation of a precursor Small SubUnit (SSU) ribosomal RNA (rRNA) molecule into a mature SSU-rRNA molecule from the pre-rRNA molecule originally produced as a tricistronic rRNA transcript that contains the Small Subunit (SSU) rRNA, 5.8S rRNA, and the Large Subunit (LSU) in that order from 5' to 3' along the primary transcript.
    GO:0006446    regulation of translational initiation    Any process that modulates the frequency, rate or extent of translational initiation.
    GO:0042255    ribosome assembly    The aggregation, arrangement and bonding together of the mature ribosome and of its subunits.
    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:0022627    cytosolic small ribosomal subunit    The small subunit of a ribosome located in the cytosol.
    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.

Chain C   (IF1A_YEAST | P38912)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003725    double-stranded RNA binding    Interacting selectively and non-covalently with double-stranded RNA.
    GO:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    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:0001732    formation of cytoplasmic translation initiation complex    Joining of the large subunit, with release of IF2/eIF2 and IF3/eIF3. This leaves the functional ribosome at the AUG, with the methionyl/formyl-methionyl-tRNA positioned at the P site.
    GO:0001731    formation of translation preinitiation complex    The joining of the small ribosomal subunit, ternary complex, and mRNA.
    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: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.

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    Glu C:120 - Glu C:121   [ RasMol ]  
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    Leu B:284 - Arg B:285   [ RasMol ]  
 
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  3wbk
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  IF1A_YEAST | P38912
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  IF2P_YEAST | P39730
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 Related Entries

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

UniProtKB/Swiss-Prot
        IF1A_YEAST | P38912: 3j80 3j81 3jam 3jap 3jaq
        IF2P_YEAST | P39730: 3wbi 3wbj 4n3s 4ncf 4v8y 4v8z

(-) Related Entries Specified in the PDB File

3wbi 3wbj