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Model Overview
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1
627

Sequence
UniProt Q9QZB6
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain
Link to: [ InterPro ]
Hormone_recep
zf-C4

Model 3D Structure
Model information:
Modelled residue range: 291 to 379
Based on template: [ 1cit ]  
Sequence Identity [%]: 92%
Model date: 2013-02-23
Revision date: 2013-01-30

Quaternary structure information: [details]
Template (1cit): MONOMER
Model: MONOMER

Ligand information: [details]
Ligands in the template: DA: 7, DC: 9, DG: 9, DT: 7, ZN: 2.
Ligands in the model: ZN: 2
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       GTCAVCGD NAACQHYGVR TCEGCKGFFK RTVQKNAKYV CLANKNCPVD
1cit_1#2  230     grcavcgd nascqhygvr tcegckgffk rtvqksakyi clankdcpvd
                                                                      
TARGET                                  hhhhhhhh hhhhh                
1cit_1#2                                hhhhhhhh hhhhh                


TARGET    49    KRRRNRCQYC RFQKCLSVGM VKEVVRTDSL KGRRGRLPSK P         
1cit_1#2  278   krrrnrcqfc rfqkclavgm vkevvrtdsl kgrrgrlpsk p-        
                                                                      
TARGET                  hh hhhhhhh                                    
1cit_1#2                hh hhhhhhh

Quality 


Template's ligands section 
Ligands in the template: DA: 7, DC: 9, DG: 9, DT: 7, ZN: 2. 
Ligands in the template that will be assessed: ZN48, ZN49. 
Model's ligands section 
ZN48 
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: 0.070 
Given the properties calculated previously, the ligand z.ZN48 will be included in the final model. 
ZN48: conservation:True, RMSD:True, included: True 
 
ZN49 
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: 0.060 
Given the properties calculated previously, the ligand z.ZN49 will be included in the final model. 
ZN49: conservation:True, RMSD:True, included: True 
 
The new model with the included ligands was saved successfully.

 
Quaternary Structure Annotation of the Template 
 1cit 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: 1cit.pdb1.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The quaternary structure can be assumed to be identical 
 Model was succesfully built as MONOMER.

Template Selection 
 - Start SMR-Pipeline for:e090f11674655f77bd48f434dcbbe2ee on BC2-cluster at Sat Feb 23 02:20:01
2013 


 - Analyze BLAST summary ... 
 - Blast template search was successfull, number of templates selected for modeling:  3
 - 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: 
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 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:4): model based on new templates
 - Send 4 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                      ***********
 - building model based on 1citA (291-379) was successful 
 -                                                    *****************************
 - building model based on 1ovlC (399-627) was successful 
 -                                               **********************************
 - building model based on 1ovlE (364-627) was successful 
 -                                      ******************************************
 - building model based on 3dzyA (293-625) was not successful go to next best template
 -                                      ******************************************
 - building model based on 3e00A (293-625) was not successful go to next best template
 -                                      ******************************************
 - building model based on 3dzuA (293-625) was not successful go to next best template
 -                                      ****************************************
 - building model based on 3dzyD (293-606) 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:e090f11674655f77bd48f434dcbbe2ee on BC2-cluster at Sat Feb 23 02:37:34
2013


Template Description
Match Chain SeqId

1cit: DNA-BINDING MECHANISM OF THE MONOMERIC ORPHAN NUCLEAR RECEPTOR NGFI-B
Solved by: X-RAY, Resolution: 2.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

291-379 1citA 92%
[Model]

2nll: RETINOID X RECEPTOR-THYROID HORMONE RECEPTOR DNA-BINDING DOMAIN HETERODIMER BOUND TO THYROID RESPONSE ELEMENT DNA
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-358 2nllA 67%
[Model]

1ovl: CRYSTAL STRUCTURE OF NURR1 LBD
Solved by: X-RAY, Resolution: 2.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

399-627 1ovlB 64%
[Model]
399-627 1ovlA 64%
[Model]
399-627 1ovlF 64%
[Model]
399-627 1ovlD 65%
[Model]
364-627 1ovlE 61%
[Model]
399-627 1ovlC 65%
[Model]

1ynw: CRYSTAL STRUCTURE OF VITMAIN D RECEPTOR AND 9-CIS RETINOICACID RECEPTOR DNA-BINDING DOMAINS BOUND TO A DR3 RESPONSEELEMENT
Solved by: X-RAY, Resolution: 3.00A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-364 1ynwB 64%
[Model]

1r0n: CRYSTAL STRUCTURE OF HETERODIMERIC ECDSYONE RECEPTOR DNA BINDING COMPLEX
Solved by: X-RAY, Resolution: 2.60A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-364 1r0nA 64%
[Model]

2han: STRUCTURAL BASIS OF HETERODIMERIC ECDYSTEROID RECEPTOR INTERACTION WITH NATURAL RESPONSE ELEMENT HSP27 GENE PROMOTER
Solved by: X-RAY, Resolution: 1.95A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-366 2hanA 62%
[Model]

1r0o: CRYSTAL STRUCTURE OF THE HETERODIMERIC ECDYSONE RECEPTOR DNA-BINDING COMPLEX
Solved by: X-RAY, Resolution: 2.24A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-366 1r0oA 62%
[Model]

1by4: STRUCTURE AND MECHANISM OF THE HOMODIMERIC ASSEMBLY OF THERXR ON DNA
Solved by: X-RAY, Resolution: 2.10A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-366 1by4A 62%
[Model]
293-366 1by4B 62%
[Model]
293-366 1by4D 62%
[Model]
293-366 1by4C 62%
[Model]

1hra: THE SOLUTION STRUCTURE OF THE HUMAN RETINOIC ACID RECEPTORBETA DNA-BINDING DOMAIN
Solved by: NMR, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-364 1hraA 61%
[Model]

1dsz: STRUCTURE OF THE RXR/RAR DNA-BINDING DOMAIN HETERODIMER INCOMPLEX WITH THE RETINOIC ACID RESPONSE ELEMENT DR1
Solved by: X-RAY, Resolution: 1.70A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-366 1dszB 62%
[Model]
293-366 1dszA 61%
[Model]

1ga5: CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV- ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT
Solved by: X-RAY, Resolution: 2.40A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-364 1ga5B 60%
[Model]
293-364 1ga5F 60%
[Model]

1a6y: REVERBA ORPHAN NUCLEAR RECEPTOR/DNA COMPLEX
Solved by: X-RAY, Resolution: 2.30A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-364 1a6yA 60%
[Model]

2a66: HUMAN LIVER RECEPTOR HOMOLOGUE DNA-BINDING DOMAIN (HLRH-1 DBD) IN COMPLEX WITH DSDNA FROM THE HCYP7A1 PROMOTER
Solved by: X-RAY, Resolution: 2.20A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-375 2a66A 60%
[Model]

1hlz: CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR REV- ERB(ALPHA) DNA-BINDING DOMAIN BOUND TO ITS COGNATE RESPONSE ELEMENT
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

293-364 1hlzB 60%
[Model]

2lze: LIGASE 10C
Solved by: NMR, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

302-364 2lzeA 25%
[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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