SWISS-MODEL Repository - Model Details

Model Overview
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1
196

Sequence
UniProt P06850 Corticoliberin (Corticotropin-releasing factor)
Homo sapiens (Human).
Database: Swiss-Prot (Reviewed) manually annotated and reviewed

STRING
P06850: 9606.ENSP0000027

Domain
Link to: [ InterPro ]
CRF

Model 3D Structure
Model information:
Modelled residue range: 154 to 194
Based on template: [ 1go9 ]  
Sequence Identity [%]: 92%
Model date: 2013-11-24
Revision date: 2013-11-19

Quaternary structure information: [details]
Template (1go9): MONOMER
Model: SINGLE CHAIN

Ligand information: [details]
Ligands in the template: ALA: 1, NH2: 1.
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 2013-11-19. 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       SEEPPISL DLTFHLLREV LEMARAEQLA QQAHSNRKLM EII       
1go9A     1       seeppisl dlth--lrev lemaraeqla qqahsnrklm eii-      
                                                                      
TARGET                 hhh hhhh        hhhhhhhhh    hhhhhhh hh        
1go9A                  hhh hh          hhhhhhhhh    hhhhhhh hh        



Quality


Template's ligands section
Ligands in the template: ALA: 1, NH2: 1.
The template contains ligands that are not yet part of the pipeline. Ligands which are currently assessed are listed in the help page.
No ligands were included in the model.


Quaternary Structure Annotation of the Template
1go9 is annotated as MONOMER
The template structure (1go9) was solved by NMR and does not contain any quaternary structure annotation
The template is annotated by the number of chains found in the PDB file

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 0.592 (>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:7b1efb02aea107aeb46b16cf20e749cf on BC2-cluster at Sun Nov 24 22:52:42
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

 - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - Skip Template HHsearch issue
 - Skip Template HHsearch issue
 - Skip Template HHsearch issue
 - Skip Template HHsearch issue
 - Skip Template HHsearch issue
 - 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 1go9A was not successful, fall back to monomeric modeling
 - building model based on 1go9A (154-194) 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:7b1efb02aea107aeb46b16cf20e749cf on BC2-cluster at Sun Nov 24 22:56:24
2013 




Template Description
Match Chain SeqId

1go9: MONITORING THE STRUCTURAL CONSEQUENCES OF PHE12-->D-PHE12 AND LEU15-->AIB15 SUBSTITUTION IN H/R CORTICOTROPIN RELEASING HORMONE: IMPLICATIONS FOR DESIGN OF CRH ANTAGONISTS.
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

154-194 1go9A 93%
[Model]

1goe: MONITORING THE STRUCTURAL CONSEQUENCES OF PHE12-->D-PHE12 AND LEU15-->AIB15 SUBSTITUTION IN H/R CORTICOTROPIN RELEASING HORMONE: IMPLICATIONS FOR DESIGN OF CRH ANTAGONISTS.
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

154-194 1goeA 93%
[Model]

2rmf: HUMAN UROCORTIN 1
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

155-194 2rmfA 43%
[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.




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