SWISS-MODEL Repository - Model Details

Model Overview
Click on the bars to get more details about individual Models or experimental structures
1
739

Sequence
UniProt Q61183
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
NTP_transf_2
PAP_RNA-bind
PAP_central

Model 3D Structure
Model information:
Modelled residue range: 19 to 498
Based on template: [ 1q79 ]  
Sequence Identity [%]: 96%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1q79): MONOMER
Model: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: 3AT: 1, ALA: 2, GOL: 4, MN: 2.
Ligands in the model: MN: 1
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       HYGITSPI SLAAPKETDC LLTQKLIETL KPFGVFEEEE ELQRRILILG
1q79A     19      hygitspi slaapketd- lltqklvetl kpfgvfeeee elqrrililg
                                                                      
TARGET                           hhh    hhhhhhhh hh      hh hhhhhhhhhh
1q79A                                  hhhhhhhhh hh      hh hhhhhhhhhh


TARGET    49    KLNNLVKEWI REISESKNLP QSVIENVGGK IFTFGSYRLG VHTKGADIDA
1q79A     67    klnnlvkewi reisesknlp qsvienvggk iftfgsyrlg vhtkgadida
                                                                      
TARGET          hhhhhhhhhh hhhhhh     hhhh     s ssss hhhh         sss
1q79A           hhhhhhhhhh hhhhhh     hhhh     s ssss hhhh         sss


TARGET    99    LCVAPRHVDR SDFFTSFYDK LKLQEEVKDL RAVEEAFVPV IKLCFDGIEI
1q79A     117   lcvaprhvdr sdfftsfydk lklqeevkdl raveeafvpv ikl-fdgiei
                                                                      
TARGET          ssssss   h hh   hhhhh hh         sss      s sss     ss
1q79A           ssssss   h hh   hhhhh hh         sss      s sss     ss


TARGET    149   DILFARLALQ TIPEDLDLRD DSLLKNLDIR CIRSLNGCRV TDEILHLVPN
1q79A     167   dilfarlalq tipedldlrd dsllknldir -irslngcrv tdeilhlvpn
                                                                      
TARGET          sssssss                hh          hhhhhhhh hhhhhh    
1q79A           sssssss                hh           hhhhhhh hhhhhh    


TARGET    199   IDNFRLTLRA IKLWAKRHNI YSNILGFLGG VSWAMLVART CQLYPNAIAS
1q79A     217   idnfrltlra iklwakrhni ysnilgflgg vswamlvart cqlypnaias
                                                                      
TARGET          hhhhhhhhhh hhhhhhh             h hhhhhhhhhh hhh     hh
1q79A           hhhhhhhhhh hhhhhhh             h hhhhhhhhhh hhh     hh


TARGET    249   TLVHKFFLVF SKWEWPNPVL LKQPEECNLN LPVWDPRVNP SDRYHLMPII
1q79A     267   tlvhkfflvf skwewpnpvl lkqpeecnln lpvwdprvnp sdryhlmpii
                                                                      
TARGET          hhhhhhhhhh hh                               hhh     ss
1q79A           hhhhhhhhhh hh                               hhh     ss


TARGET    299   TPAYPQQNST YNVSVSTRMV MVEEFKQGLA ITDEILLSKA EWSKLFEAPN
1q79A     317   tpaypqqnst ynvsvstrmv mveefkqgla itdeillska ewsklfeapn
                                                                      
TARGET          s     sss      hhhhhh hhhhhhhhhh hhhhhhh      hhhh    
1q79A           s     sss      hhhhhh hhhhhhhhhh hhhhhhh      hh      


TARGET    349   FFQKYKHYIV LLASAPTEKQ RLEWVGLVES KIRILVGSLE KNEFITLAHV
1q79A     367   ffqkykhyiv llasaptekq rlewvglves kirilvgsle knefitlahv
                                                                      
TARGET               sssss sssss  hhh hhhhhhhhhh hhhhhhhhhh h  sssssss
1q79A                sssss sssss  hhh hhhhhhhhhh hhhhhhhhhh    sssssss


TARGET    399   NPQSFPAPKE SPDREEFRTM WVIGLVFKKT ENSENLSVDL TYDIQSFTDT
1q79A     417   npqsfpapke npdkeefrtm wviglvfk-- --------dl tydiqsftdt
                                                                      
TARGET          s   sss          ssss ssssssss h hh         hhhhhhhhhh
1q79A           s   sss          ssss ssssssss              hhhhhhhhhh


TARGET    449   VYRQAINSKM FELDMKIAAM HVKRKQLHQL LP                   
1q79A     467   vyrqainskm fevdmkiaam hvkrkqlhql lp-                  
                                                                      
TARGET          hhhhhhh         sssss ssss                            
1q79A           hhhhhhh         sssss ssss

Quality 


Template's ligands section 
Ligands in the template: 3AT: 1, ALA: 2, GOL: 4, MN: 2. 
Ligands in the template that will be assessed: MN1001, MN1002. 
Model's ligands section 
MN1001 
All the residues interacting with the ligand are completely conserved between model and template. 
The RMSD between the interacting residues of model and template is smaller than 2 Angstrom: 0.300 
Given the properties calculated previously, the ligand MN1001 will be included in the final model. 
MN1001: conservation:True, RMSD:True, included: True 
 
MN1002 
The ligand binds less than 3 template residues. 
Given the properties calculated previously, the ligand MN1002 will not be included in the final model. 
MN1002: conservation:False, RMSD:False, included: False 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 1q79 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: 1q79.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 Analysis of evolutionary and family specific aspects revealed conservation of the oligomeric structure 
 Hence, the oligomeric structures of the target and the template can be assumed to be similar (=MONOMER) 
 The corresponding reliability score is 0.632 (>0.5 indicates similarity) 
 Unfortunately, we were not able to built the model as MONOMER. 
 Thus, the model was built as single chain.

Template Selection 
 - Start SMR-Pipeline for:2d03cc3a10e882b534f084851d6c6fde on BC2-cluster at Sat Feb 23 05:18:08
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  1
 - But still uncovered regions of the target sequence detected, go for: HHSEARCH

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with D found
 - No template with C found
 - No template with C found
 - No template with D 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

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -   ****************************************************
 - Oligomeric modeling of 1q79A was not successful, fall back to monomeric modeling
 - building model based on 1q79A (19-498) 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:2d03cc3a10e882b534f084851d6c6fde on BC2-cluster at Sat Feb 23 05:21:04
2013


Template Description
Match Chain SeqId

1q78: CRYSTAL STRUCTURE OF POLY(A) POLYMERASE IN COMPLEX WITH 3'DATP AND MAGNESIUM CHLORIDE
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

19-498 1q78A 97%
[Model]

1f5a: CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE
Solved by: X-RAY, Resolution: 2.50A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

20-498 1f5aA 96%
[Model]

1q79: CRYSTAL STRUCTURE OF MAMMALIAN POLY(A) POLYMERASE
Solved by: X-RAY, Resolution: 2.15A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

19-498 1q79A 96%
[Model]

1fa0: STRUCTURE OF YEAST POLY(A) POLYMERASE BOUND TO MANGANATE AND 3'-DATP
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

17-499 1fa0A 40%
[Model]
17-501 1fa0B 40%
[Model]

2hhp: STRUCTURE OF YEAST POLY(A) POLYMERASE IN A CLOSED CONFORMATION.
Solved by: X-RAY, Resolution: 1.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

17-501 2hhpA 40%
[Model]

3c66: YEAST POLY(A) POLYMERASE IN COMPLEX WITH FIP1 RESIDUES 80-105
Solved by: X-RAY, Resolution: 2.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

17-504 3c66A 38%
[Model]
17-503 3c66B 39%
[Model]

2o1p: STRUCTURE OF YEAST POLY(A) POLYMERASE IN A SOMEWHAT CLOSEDSTATE
Solved by: X-RAY, Resolution: 2.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

17-502 2o1pA 39%
[Model]
17-501 2o1pB 39%
[Model]

2q66: STRUCTURE OF YEAST POLY(A) POLYMERASE WITH ATP AND OLIGO(A
Solved by: X-RAY, Resolution: 1.80A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

18-501 2q66A 39%
[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.