SWISS-MODEL Repository - Model Details

Model Overview
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1
263

Sequence
UniProt P22090
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P22090: 9606.ENSP0000025

Domain
Link to: [ InterPro ]
KOW
Ribosomal_S4e
S4
RS4NT

Model 3D Structure
Model information:
Modelled residue range: 2 to 259
Based on template: [ 3u5c ]  
Sequence Identity [%]: 70%
Model date: 2013-04-22
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (3u5c): MONOMER
Model built: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: none.
Ligands in the model: none.
Template Links: [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  
display model: in [ AstexViewer ]
download model: as [ pdb ] - as [ Deepview project ]

Alignment 

TARGET    1       ARGPKKHL KRVAAPKHWM LDKLTGVFAP RPSTGPHKLR ECLPLIVFLR
3u5cE     2       argpkkhl krlaaphhwl ldklsgcyap rpsagphklr eslplivflr
                                                                      
TARGET                   s ss               sss                 hhhhh 
3u5cE                    s ss               sss                 hhhhh 


TARGET    49    NRLKYALTGD EVKKICMQRF IKIDGKVRVD VTYPAGFMDV ISIEKTGEHF
3u5cE     50    nrlkyalngr evkailmqrh vkvdgkvrtd ttypagfmdv itldatnenf
                                                                      
TARGET                   h hhhhhh      sss               ss ssss  ssss
3u5cE                    h hhhhhhh     sss               ss ssss  ssss


TARGET    99    RLVYDTKGRF AVHRITVEEA KYKLCKVRKI TVGVKGIPHL VTHDARTIRY
3u5cE     100   rlvydvkgrf avhritdeea syklgkvkkv qlgkkgvpyv vthdgrtiry
                                                                      
TARGET          ss           sss        ssssssss sss   ssss sss  sssss
3u5cE           ss           sss        ssssssss sss   ssss sss  sssss


TARGET    149   PDPVIKVNDT VQIDLGTGKI INFIKFDTGN LCMVIGGANL GRVGVITNRE
3u5cE     150   pdpnikvndt vkidlasgki tdfikfdagk lvyvtggrnl grigtivhke
                                                                      
TARGET                  ss ssss    ss ssss       sssss       sss   sss
3u5cE                   ss ssss    ss ssss       sssss       sss   sss


TARGET    199   RHPGSFDVVH VKDANGNSFA TRLSNIFVIG NGNKPWISLP RGKGIRLTVA
3u5cE     200   rhdggfdlvh ikdsldntfv trlnnvfvig eqgkpyislp kgkgiklsia
                                                                      
TARGET                ssss sss   ssss sss ssssss s  sss             hh
3u5cE                 ssss sss   ssss sss ssssss s  sss             hh


TARGET    249   EERDKRLATK  -                                         
3u5cE     250   eerdrrraqq gl                                         
                                                                      
TARGET          hhhhhh                                                
3u5cE           hhhhhhh

Quality 


Template's ligands section 
Template without ligands. 
No ligands were included in the model.

 
Quaternary Structure Annotation of the Template 
 3u5c is annotated as MONOMER 
 PISA was used to annotate the quaternary structure, because the author assignment was 
  The template was built based on the following PISA annotation file: 3u5c_assembly.xml.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed non-conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template cannot be assumed to be similar (=MONOMER) 
 The target structure was calculated as SINGLE CHAIN 
 The corresponding reliability score is 0.348 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:6b3784a11d28f5c34d130e1b7b270f3c on BC2-cluster at Mon Apr 22 09:18:18
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1 go for
modeling ...

 - No A3m found

 - No template with A found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with I found
 - No template with J found
 - No template with K found
 - No template with L found
 - No template with M found
 - No template with N found
 - No template with O found
 - No template with P found
 - No template with Q found
 - No template with R found
 - No template with S found
 - No template with T found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with a found
 - No template with b found
 - No template with c found
 - No template with d found
 - No template with e found
 - No template with f found
 - No template with g found
 - No template with h found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:1): model based on new templates
 - Send 1 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -  ******************************************************************************
 - building model based on 3u5cE (2-259) was successful 
 - Repository Pipeline parameter

   Cut-off parameters to model the target based on a BLAST target-template alignment
    Evalue :                                     0.0001
    Minimum Template size (aa) for ranking :     25
    Minimum Sequence identity :                  60

   Cut-off parameters to model the target based on a HHSearch target-template alignment
    Evalue :                                     0.0001
    Probability :                                50
    MAC :                                        0.3

   Parameters for model selection
    Minimal number of uncovered target
     residues after BLAST to run HHSEARCH :      50
    Minimal number of uncovered target
     residues to model an additional template :  25
    
 - Finish SMR-Pipeline for:6b3784a11d28f5c34d130e1b7b270f3c on BC2-cluster at Mon Apr 22 09:19:26
2013


Template Description
Match Chain SeqId

3u5g: THE STRUCTURE OF THE EUKARYOTIC RIBOSOME AT 3.0 A RESOLUTI
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-259 3u5gE 71%
[Model]

3u5c: THE STRUCTURE OF THE EUKARYOTIC RIBOSOME AT 3.0 A RESOLUTI
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

2-259 3u5cE 71%
[Model]

3iz6: LOCALIZATION OF THE SMALL SUBUNIT RIBOSOMAL PROTEINS INTO CRYO-EM MAP OF TRITICUM AESTIVUM TRANSLATING 80S RIBOSOME
Solved by: X-RAY, Resolution: 5.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

43-242 3iz6D 67%
[Model]

Downloads
Reference

If you are using models from the SWISS-MODEL Repository, please cite the following articles:

- Kiefer F, Arnold K, Künzli M, Bordoli L, Schwede T (2009).
The SWISS-MODEL Repository and associated resources.
Nucleic Acids Res. 37, D387-D392.

- Jürgen Kopp and Torsten Schwede (2004)
The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models.
Nucleic Acids Res. 32, D230-D234.
SWISS-MODEL is developed by the Protein Structure Bioinformatics group at the SIB - Swiss Institute of Bioinformatics & the Biozentrum University of Basel. © 2011.