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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF EUKARYOTIC TRANSLATION INITIATION FACTOR 5B STRUCTURE II
 
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 :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Flexible, Eukaryotic Translation Initiation, Eif1A, 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
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDBHT2
    Expression System StrainB834-CODONPLUS(DE3)-RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 401-855
    GeneFUN12, YAL035W
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid559292
    StrainATCC 204508 / S288C
    SynonymEIF-5B, TRANSLATION INITIATION FACTOR IF-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 3WBJ)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:9 -A:94

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:301 -Ala A:302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WBJ)

(-) 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:445
 aligned with IF2P_YEAST | P39730 from UniProtKB/Swiss-Prot  Length:1002

    Alignment length:455
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850     
           IF2P_YEAST   401 KDLRSPICCILGHVDTGKTKLLDKIRQTNVQGGEAGGITQQIGATYFPIDAIKAKTKVMAEYEKQTFDVPGLLVIDTPGHESFSNLRSRGSSLCNIAILVIDIMHGLEQQTIESIKLLRDRKAPFVVALNKIDRLYDWKAIPNNSFRDSFAKQSRAVQEEFQSRYSKIQLELAEQGLNSELYFQNKNMSKYVSIVPTSAVTGEGVPDLLWLLLELTQKRMSKQLMYLSHVEATILEVKVVEGFGTTIDVILSNGYLREGDRIVLCGMNGPIVTNIRALLTPQPLRELRLKSEYVHHKEVKAALGVKIAANDLEKAVSGSRLLVVGPEDDEDELMDDVMDDLTGLLDSVDTTGKGVVVQASTLGSLEALLDFLKDMKIPVMSIGLGPVYKRDVMKASTMLEKAPEYAVMLCFDVKVDKEAEQYAEQEGIKIFNADVIYHLFDSFTAYQEKLLEERR 855
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee....hhhhhhhhhhh.ee..ee....ee...eeeeehhhhhhhhhhhh..........eeeee...---..............eeeeeee.....hhhhhhhhhhhhhh...eeeeeehhhhh.........hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eee.hhh......eeeee.......hhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeee...eeeeeeeeee.eee....eee........-.eeeeeee...------..eeee.eee..eeeeeee...........eee.....hhhhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh..hhhh.eeeee....hhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wbj A   1 KDLRSPICCILGHVDTGKTKLLDKIRQTNVQGGEAGGITQQIGATYFPIDAIKAKTKVMAEYEKQTFDVPGLLVIDTP---SFSNLRSRGSSLCNIAILVIDIMHGLEQQTIESIKLLRDRKAPFVVALNKIDRLYDWKAIPNNSFRDSFAKQSRAVQEEFQSRYSKIQLELAEQGLNSELYFQNKNMSKYVSIVPTSAVTGEGVPDLLWLLLELTQKRMSKQLMYLSHVEATILEVKVVEGFGTTIDVILSNGYLREGDRIVLCGMNGPIV-NIRALLTPQPL------SEYVHHKEVKAALGVKIAANDLEKAVSGSRLLVVGPEDDEDELMDDVMDDLTGLLDSVDTTGKGVVVQASTLGSLEALLDFLKDMKIPVMSIGLGPVYKRDVMKASTMLEKAPEYAVMLCFDVKVDKEAEQYAEQEGIKIFNADVIYHLFDSFTAYQEKLLEERR 455
                                    10        20        30        40        50        60        70       | - |      90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270 | |   280   |     -|      300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450     
                                                                                                        78  82                                                                                                                                                                                           272 |       284    291                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                           274                                                                                                                                                                                     

   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 3WBJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

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  Cis Peptide Bonds
    Ala A:301 - Ala A:302   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        IF2P_YEAST | P397303wbi 3wbk 4n3s 4ncf 4v8y 4v8z

(-) Related Entries Specified in the PDB File

3wbi 3wbk