SWISS-MODEL Repository - Model Details

Model Overview
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1
482

Sequence
UniProt P21827
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
P21827: 4932.YGL097W

Domain
Link to: [ InterPro ]
RCC1
RCC1
RCC1
RCC1_2
RCC1_2

Model 3D Structure
Model information:
Modelled residue range: 27 to 482
Based on template: [ 3of7 ]  
Sequence Identity [%]: 95%
Model date: 2013-02-18
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (3of7): 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 ]

This model has not been updated since 2013-01-30. In the meantime, new template structures may have become available which would allow building a more reliable model. Would you like to submit the target protein to SWISS-MODEL Workspace and build a new model now? [ Submit ]



Alignment 

TARGET    1        SHIINAQ EDYKHMYLSV QPLDIFCWGT GSMCELGLGP LAKNKEVKRP
3of7A     26    m--shiinaq edykhmylsv qpldifcwgt gsmcelglgp laknkevkrp
                                                                      
TARGET                         hhh       sssssss s              sss   
3of7A                      hhhhh         sssssss s              sss   


TARGET    48    RLNPFLPRDE AKIISFAVGG MHTLALDEES NVWSWGCNDV GALGRDTSNA
3of7A     74    rlnpflprde akiisfavgg mhtlaldees nvwswgcndv galgrdts--
                                                                      
TARGET          sss         ssssssss  ssssssss   sssssss              
3of7A           sss         ssssssss  ssssssss   sssssss              


TARGET    98    KEQLKDMDAD DSSDDEDGDL NELESTPAKI PRESFPPLAE GHKVVQLAAT
3of7A     143   ---------- ---------l nelestpaki presfpplae ghkvvqlaat
                                                                      
TARGET              hhhhh              hhhh  sss       hhhh   ssssssss
3of7A                                  hhhh  sss       hhh    ssssssss


TARGET    148   DNMSCALFSN GEVYAWGTFR CNEGILGFYQ DKIKIQKTPW KVPTFSKYNI
3of7A     174   dnmscalfsn gevyawgtfr cnegilgfyq dkikiqktpw kvptfskyni
                                                                      
TARGET           ssssssss   sssssssss s  sss              s ss      ss
3of7A            ssssssss   sssssssss s  sss              s ss      ss


TARGET    198   VQLAPGKDHI LFLDEEGMVF AWGNGQQNQL GRKVMERFRL KTLDPRPFGL
3of7A     224   vqlapgkdhi lfldeegmvf awgngqqnql grkvmerfrl ktldprpfgl
                                                                      
TARGET          ssssss sss sssss ssss ssss                h h        s
3of7A           ssssss sss sssss ssss ssss                h h        s


TARGET    248   RHVKYIASGE NHCFALTKDN KLVSWGLNQF GQCGVSEDVE DGALVTKPKR
3of7A     274   rhvkyiasge nhcfaltkdn klvswglnqf gqcgvsedve dgalvtkpkr
                                                                      
TARGET          sssssssss  ssssssss   ssssssss                sss   ss
3of7A           sssssssss  ssssssss   ssssssss                sss   ss


TARGET    298   LALPDNVVIR SIAAGEHHSL ILSQDGDLYS CGRLDMFEVG IPKDNLPEYT
3of7A     324   lalpdnvvir siaagehhsl ilsqdgdlys cgrldmfevg ipkdnlpeyt
                                                                      
TARGET          s      sss sssss ssss ssss  ssss ssss                 
3of7A           s      sss sssss ssss ssss  ssss ssss                 


TARGET    348   YKDVHGKARA VPLPTKLNNV PKFKSVAAGS HHSVAVAQNG IAYSWGFGET
3of7A     374   ykdvhgkara vplptklnnv pkfksvaags hhsvavaqng iayswgfget
                                                                      
TARGET          sss   ssss s   sss     ssssssss  ssssssss   sssssss   
3of7A           sss   ssss s   sss     ssssssss  ssssssss   sssssss   


TARGET    398   YAVGLGPFED DTEVPTRIKN TATQDHNIIL VGCGGQFSVS GGVKLSDEDA
3of7A     424   yavglgpfed dtevptrikn tatqdhniil vgcggqfsvs ggvklsdeda
                                                                      
TARGET                          sss       ssssss ssss sssss sssss hhhh
3of7A                           sss       ssssss ssss sssss sssss hhhh


TARGET    448   EKRADEMDD                                             
3of7A     474   ekrademddl                                            
                                                                      
TARGET          hhhhhhhh                                              
3of7A           hhhhhhhh

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3of7 is annotated as MONOMER 
 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: 3of7.pdb1.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 0.178 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:be2b40976724a1cefde344db3305679c on BC2-cluster at Mon Feb 18 17:52:28
2013 


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

 - 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 3of7A (27-482) 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:be2b40976724a1cefde344db3305679c on BC2-cluster at Mon Feb 18 17:54:15
2013


Template Description
Match Chain SeqId

3of7: THE CRYSTAL STRUCTURE OF PRP20P FROM SACCHAROMYCES CEREVISBINDING PROPERTIES TO GSP1P AND HISTONES
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

27-482 3of7A 95%
[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.