Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE EIF3B-CTD/EIF3I/EIF3G-NTD TRANSLATION INITIATION COMPLEX
 
Authors :  S. Zhang, J. P. Erzberger, T. Schaefer, N. Ban
Date :  15 Jul 14  (Deposition) - 10 Sep 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  B,G,I
Keywords :  Translation Initiation, Eif3 Complex, Beta-Propeller, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. P. Erzberger, F. Stengel, R. Pellarin, S. Zhang, T. Schaefer, C. H. Aylett, P. Cimermancic, D. Boehringer, A. Sali, R. Aebersold, N. Ban
Molecular Architecture Of The 40Seif1Eif3 Translation Initiation Complex.
Cell V. 158 1123 2014
PubMed-ID: 25171412  |  Reference-DOI: 10.1016/J.CELL.2014.07.044

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT I
    Chains: I
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: PRIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TIF34, SCY_4321
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 307796
    Strain: YJM789
    Synonym: EIF3I,EUKARYOTIC TRANSLATION INITIATION FACTOR 3 39 KDA SUBUNIT HOMOLOG,EIF-3 39 KDA SUBUNIT HOMOLOG
 
Molecule 2 - EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PRT1, CDC63, YOR361C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    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
 
Molecule 3 - EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT G
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TIF35, YDR429C, D9461.16
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: EIF3G,EUKARYOTIC TRANSLATION INITIATION FACTOR 3 RNA-BINDING SUBUNIT,EIF-3 RNA-BINDING SUBUNIT,TRANSLATION INITIATION FACTOR EIF3 P33 SUBUNIT,EIF3 P33

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : BGI

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4U1E)

(-) Sites  (0, 0)

(no "Site" information available for 4U1E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U1E)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gln B:697 -Pro B:698
2Asp G:14 -Gly G:15
3Lys G:62 -Gly G:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U1E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U1E)

(-) Exons   (0, 0)

(no "Exon" information available for 4U1E)

(-) 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 B from PDB  Type:PROTEIN  Length:47
                                                                               
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                 4u1e B 652 SNAEADTAMRDLILHQRELLKQWTEYREKIGQEMEKSMNFKIFDVQP 698
                                   661       671       681       691       


Chain G from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eeeeeeeee..eeeeeeeee.........hhhhhhhhh...hhhhh..............ee.......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 4u1e G   8 EIIENADGSRSIITYKIEDGVKYKITQKVKEVKVLEKVHKSVAERKNWHKYGSEKGSPAGPSAVTARLGEEVELRLSRNWKQAEEERIQ  96
                                    17        27        37        47        57        67        77        87         


Chain I from PDB  Type:PROTEIN  Length:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee......eeeeee.....eeeeee....eeeee.....eeeee......eeeeee.....eeeeee...eeeeee.....eeeeee....eeeeee.....eeeeee........eeeeeeeee......eeee.....eeee.......eeeeee.hhh.eeeeee....eeeee.....eeeeee......eeeeee.....eeeeee...eeeeee.....eeeeee....eeeeee.....eeeeee....eeeeeee.....eeeeeeee...eeeeee.....eeeeee....eeeee.hhhhhhh.hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4u1e I   1 MKAIKLTGHERPLTQVKYNKEGDLLFSCSKDSSASVWYSLNGERLGTLDGHTGTIWSIDVDCFTKYCVTGSADYSIKLWDVSNGQCVATWKSPVPVKRVEFSPCGNYFLAILDNVMKNPGSINIYEIERDSATHELTKVSEEPIHKIITHEGLDAATVAGWSTKGKYIIAGHKDGKISKYDVSNNYEYVDSIDLHEKSISDMQFSPDLTYFITSSRDTNSFLVDVSTLQVLKKYETDCPLNTAVITPLKEFIILGGGQGKFEARFYHKIFEEEIGRVQGHFGPLNTVAISPQGTSYASGGEDGFIRLHHFEKSYFDFKYDVEKAAEAKEH 342
                                    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       272       282       292       302       312       322       332       342
                                                                                                                                                                                                                                                                                           258|                                                                       
                                                                                                                                                                                                                                                                                            271
   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 4U1E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U1E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U1E)

(-) Gene Ontology  (20, 56)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4u1e)
 
  Sites
(no "Sites" information available for 4u1e)
 
  Cis Peptide Bonds
    Asp G:14 - Gly G:15   [ RasMol ]  
    Gln B:697 - Pro B:698   [ RasMol ]  
    Lys G:62 - Gly G:63   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4u1e
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EIF3A_YEAST | P38249
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  EIF3B_YEAST | P06103
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  EIF3G_YEAST | Q04067
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  EIF3I_YEAS7 | A6ZMK5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  EIF3A_YEAST | P38249
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  EIF3B_YEAST | P06103
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  EIF3G_YEAST | Q04067
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  EIF3I_YEAS7 | A6ZMK5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EIF3A_YEAST | P38249: 3jap 4k51 4u1c 4u1d
        EIF3B_YEAST | P06103: 3jap 3jaq 3ns5 3ns6 3zwl 4u1f
        EIF3G_YEAST | Q04067: 3jap 3jaq

(-) Related Entries Specified in the PDB File

4u1c 4u1d 4u1f