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 :  EIF3B RELOCATED TO THE INTERSUBUNIT FACE TO INTERACT WITH EIF1 AND BELOW THE EIF2 TERNARY-COMPLEX. FROM THE STRUCTURE OF A PARTIAL YEAST 48S PREINITIATION COMPLEX IN CLOSED CONFORMATION.
 
Authors :  A. Simonetti, J. Brito Querido, A. G. Myasnikov, E. Mancera-Martinez A. Renaud, L. Kuhn, Y. Hashem
Date :  18 May 16  (Deposition) - 13 Jul 16  (Release) - 03 Aug 16  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  4.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Eukaryotic Translation Initiation, Ribosome, Eif3 Peripheral Subunits, Cryo-Em, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Simonetti, J. Brito Querido, A. G. Myasnikov, E. Mancera-Martinez, A. Renaud, L. Kuhn, Y. Hashem
Eif3 Peripheral Subunits Rearrangement After Mrna Binding And Start-Codon Recognition.
Mol. Cell V. 63 206 2016
PubMed-ID: 27373335  |  Reference-DOI: 10.1016/J.MOLCEL.2016.05.033

(-) Compounds

Molecule 1 - EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT B
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System CommonHUMAN
    Expression System Taxid9606
    FragmentUNP RESIDUES 170-745
    GeneEIF3B, EIF3S9
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEIF3B,EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 9, PRT1 HOMOLOG,HPRT1,EIF-3-ETA,EIF3 P110,EIF3 P116
 
Molecule 2 - EIF3A C-TERMINAL TAIL
    ChainsA
    EngineeredYES
    Expression SystemORYCTOLAGUS CUNICULUS
    Expression System CommonRABBIT
    Expression System Taxid9986
    Organism CommonRABBIT
    Organism ScientificORYCTOLAGUS CUNICULUS
    Organism Taxid9986

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 54)

Asymmetric/Biological Unit (1, 54)
No.NameCountTypeFull Name
1UNK54Mod. Amino Acid

(-) Sites  (0, 0)

(no "Site" information available for 5K1H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K1H)

(-) Cis Peptide Bonds  (14, 14)

Asymmetric/Biological Unit
No.Residues
1Cys B:205 -Arg B:206
2Ser B:210 -Val B:211
3Ser B:215 -Gly B:216
4Asp B:303 -Pro B:304
5Ser B:326 -Ala B:327
6Trp B:329 -Pro B:330
7Thr B:354 -Pro B:355
8Gly B:379 -Asn B:380
9Leu B:401 -Pro B:402
10Ala B:487 -Pro B:488
11Asn B:535 -Gly B:536
12Gly B:536 -Ala B:537
13Thr B:543 -Ser B:544
14Lys B:647 -Glu B:648

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K1H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K1H)

(-) Exons   (0, 0)

(no "Exon" information available for 5K1H)

(-) 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:54
                                                                                      
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 5k1h A   1 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx  54
                            ||||||||10||||||||20||||||||30||||||||40||||||||50||||
                            ||||||||9-UNK|||18-UNK|||27-UNK|||36-UNK|||45-UNK|||54-UNK
                            1-UNK|||10-UNK|||19-UNK|||28-UNK|||37-UNK|||46-UNK||| 
                             2-UNK|| 11-UNK|| 20-UNK|| 29-UNK|| 38-UNK|| 47-UNK|| 
                              3-UNK|  12-UNK|  21-UNK|  30-UNK|  39-UNK|  48-UNK| 
                               4-UNK   13-UNK   22-UNK   31-UNK   40-UNK   49-UNK 
                                5-UNK   14-UNK   23-UNK   32-UNK   41-UNK   50-UNK
                                 6-UNK   15-UNK   24-UNK   33-UNK   42-UNK   51-UNK
                                  7-UNK   16-UNK   25-UNK   34-UNK   43-UNK   52-UNK
                                   8-UNK   17-UNK   26-UNK   35-UNK   44-UNK   53-UNK

Chain B from PDB  Type:PROTEIN  Length:554
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeee.......hhhhhhhhhhhhhhhhh..eeeee..hhhhh...eeeeee..hhhhhhhhhhh..ee.....ee........................hhhhhhhhhhhhhh....eeeeeee....eeeeeee......eeeeee......eee......eeeee..eeeeee....eeeeee......eeee.....eeeee............eeeee.....eeeee...........ee.....eeeeee..eeeeee....ee.hhh........eeee.....eeeeee........eeeeee....eeeeeee...eeeeeeee.....eeeeeeee........eeeeeeee.......eeeeeee..eeeeee......eeeee.....eeeeeeee.....eeeeeeeeee...eeee.....eeeee.......eeeeee....eeeeeee.....eeee.....eeeee..........eeeeee...eeeeeee.....eeee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k1h B  73 GDVLKDRPQEADGIDSVIVVDNVPQVGPDRLEKLKNVIHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNLFTDFDKYMTISDEWDIPEKQPFKDLGNLRYWLEEAECRDQYSVIFESGDRTSIFWNDVKDPVSIEERARWTETYVRWSPKGTYLATFHQRGIALWGGEKFKQIQRFSHQGVQLIDFSPCERYLVTFSPLMDTQDDPQAIIIWDILTGHKKRGFHCESSAHWPIFKWSHDGKFFARMTLDTLSIYETPSMGLLDKKSLKISGIKDFSWSPGGNIIAFWVPEDKDIPARVTLMQLPSRQEIRVRNLFNVVDCKLHWQKNGDYLCVKVDRTPKGTQGVVTNFEIFRMREKQVPVDVVEMKETIIAFAWEPNGSKFAVLHGEAPRISVSFYHVKSNGKIELSKMFDKQQANTIFWSPQGQFVVLAGLRSMNGALAFVDTSDCTVMNIAEHYMASDVEWDPTGRYVVTSVSWWSHKVDNAYWLWTFQGRLLQKNNKDRFCQLLWRPRIFEQKDRLSQSKASKE 648
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       634       644    
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   610|               
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    633               

   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 5K1H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K1H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K1H)

(-) Gene Ontology  (21, 21)

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
    UNK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 5k1h)
 
  Cis Peptide Bonds
    Ala B:487 - Pro B:488   [ RasMol ]  
    Asn B:535 - Gly B:536   [ RasMol ]  
    Asp B:303 - Pro B:304   [ RasMol ]  
    Cys B:205 - Arg B:206   [ RasMol ]  
    Gly B:379 - Asn B:380   [ RasMol ]  
    Gly B:536 - Ala B:537   [ RasMol ]  
    Leu B:401 - Pro B:402   [ RasMol ]  
    Lys B:647 - Glu B:648   [ RasMol ]  
    Ser B:210 - Val B:211   [ RasMol ]  
    Ser B:215 - Gly B:216   [ RasMol ]  
    Ser B:326 - Ala B:327   [ RasMol ]  
    Thr B:354 - Pro B:355   [ RasMol ]  
    Thr B:543 - Ser B:544   [ RasMol ]  
    Trp B:329 - Pro B:330   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5k1h
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EIF3B_HUMAN | P55884
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  EIF3B_HUMAN | P55884
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EIF3B_HUMAN | P558842krb 2nlw

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5K1H)