SWISS-MODEL Repository - Model Details

Model Overview
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1
246

Sequence
UniProt Q9NEN6
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9NEN6: 6239.Y71A12B.1

Domain
Link to: [ InterPro ]
Ribosomal_S6e

Model 3D Structure
Model information:
Modelled residue range: 1 to 219
Based on template: [ 3u5g ]  
Sequence Identity [%]: 55%
Model date: 2013-05-06
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (3u5g): HETERO 34-mer
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       MRLNFAYP ATGLQKSFEV DEEKKLRLFF EKRMSQEVAI DALGDEWKGY
3u5gG     1       mklnisyp vngsqktfei ddehrirvff dkrigqevdg eavgdefkgy
                                                                      
TARGET            ssssssss   ssssssss   hhhhhh    sss sssss hh       s
3u5gG             ssssssss   ssssssss   hhhhhh    sss sssss hh       s


TARGET    49    VVRIGGGNDK QGFPMKQGIL TNGRVRLLLK KGQSCYRERK NGERKRKSVR
3u5gG     49    vfkisggndk qgfpmkqgvl lptriklllt knvscyrprr dgerkrksvr
                                                                      
TARGET          ssssssssss   sss      sssssssss                 ssssss
3u5gG           ssssssssss   sss      sssssssss                 ssssss


TARGET    99    GCIVDANMSA LSLVIVKKGD GEIEGLTDSV LPRKLGPKRA SKIRKLFNLT
3u5gG     99    gaivgpdlav lalvivkkge qelegltdtt vpkrlgpkra nnirkffgls
                                                                      
TARGET          ssss  ssss ssssss                         h hhhhhhh   
3u5gG           ssss  ssss ssssss                         h hhhhhhh   


TARGET    149   KHDDVTKYVI THDKTFPDGV TKTIAPKIQR LITPARIARK KYLLRQKRNQ
3u5gG     149   keddvrdfvi rrevtkgek- tytkapkiqr lvtpqrlqrk rhqralkvrn
                                                                      
TARGET                      sss        sss          hhhhhhh hhhhhhhhhh
3u5gG                       sssss  s  ssss          hhhhhhh hhhhhhhhhh


TARGET    199   KIKMRDDAAA YHKLLAKYSK E                               
3u5gG     198   aqaqreaaae yaqllakrls e-                              
                                                                      
TARGET          hhhhhhhhhh hhhhhhh                                    
3u5gG           hh   hhhhh hhhhhhh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3u5g is annotated as HETERO 34-mer 
 The oligomeric state of the structure was assigned by the authors of the corresponding PDB entry 
 The following biological unit was used to build the template structure: 3u5g.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3u5g_1

Template Selection 
 - Start SMR-Pipeline for:bd9d9f1750a9bdc4acfe63043d35e106 on BC2-cluster at Mon May  6 17:51:45
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - 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 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
 - 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 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 3u5gG (1-219) 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:bd9d9f1750a9bdc4acfe63043d35e106 on BC2-cluster at Mon May  6 17:57:55
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 HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-219 3u5gG 56%
[Model]

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

1-225 3u5cG 55%
[Model]

2xzm: CRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMPLEX WITH INITIATION FACTOR 1. THIS FILE CONTAINS THE 40S SUBUNIT AND INITIATION FACTOR FOR MOLECULE 1
Solved by: X-RAY, Resolution: 3.93A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-225 2xzmY 52%
[Model]

2xzn: CRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMPLEX WITH INITIATION FACTOR 1. THIS FILE CONTAINS THE 40S SUBUNIT AND INITIATION FACTOR FOR MOLECULE 2
Solved by: X-RAY, Resolution: 3.93A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-225 2xznY 52%
[Model]

3zey: HIGH-RESOLUTION CRYO-ELECTRON MICROSCOPY STRUCTURE OF THE BRUCEI RIBOSOME
Solved by: X-RAY, Resolution: 5.57A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-243 3zey3 40%
[Model]

3j20: PROMISCUOUS BEHAVIOR OF PROTEINS IN ARCHAEAL RIBOSOMES REVCRYO-EM: IMPLICATIONS FOR EVOLUTION OF EUKARYOTIC RIBOSOMRIBOSOMAL SUBUNIT)
Solved by: X-RAY, Resolution: 6.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

1-114 3j20G 28%
[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.