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Model Overview

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201

Sequence

UniProt

Q38896

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

Q38896: 3702.AT2G21060.1

Domain

Link to: [ InterPro ]

	zf-CCHC
	zf-CCHC
	CSD

Model 3D Structure

	Model information:
	Modelled residue range:	16 to 65
	Based on template:	[ 3i2z ]
	Sequence Identity [%]:	57%
	Model date:	2013-02-19
	Revision date:	2013-01-30

Quaternary structure information:	[details]
Template (3i2z): 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         KGTVKW FDTQKGFGFI TPSDGGDDLF VHQSSIRSEG FRSLAAEESV
3i2zB     3     ki--kgnvkw fneskgfgfi tpedgskdvf vhfsaiqtng fktlaegqrv
                                                                      
TARGET              ssssss sss  sssss sss     ss sss               sss
3i2zB            s  ssssss ss   sssss sss     ss sss               sss


TARGET    47    EFDV ----- ---------                                  
3i2zB     51    efeitngakg psaanvtal                                  
                                                                      
TARGET                                                                
3i2zB           sssssss  s ssss  sss

Quality

[ start new quality assessment in Workspace ]

Ligand Modelling Log

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

Oligomer Modelling Log

Quaternary Structure Annotation of the Template 
 3i2z is annotated as MONOMER 
 PISA was used to annotate the quaternary structure, because the author assignment was ambigous (i.e the same chains appear in different biolgoical units annotated by the author) 
 PISA annotates this structure as Monomer, therefore the corresponding PDB chain was used as template structure 
      
 
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 0.486 (>0.5 indicates similarity)

Template Selection

 - Start SMR-Pipeline for:a3c5327c506368613c8216aba74c7bdd on BC2-cluster at Tue Feb 19 22:56:40
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 modfied template library 
 - Summarize templates: 
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:3): model based on new templates
 - Send 3 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -       ********************
 - building model based on 3i2zB (16-65) was successful 
 -        *********************************
 - building model based on 3trzB (17-98) was successful 
 -                                                        *************************
 - building model based on 2exfA (137-200) 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:a3c5327c506368613c8216aba74c7bdd on BC2-cluster at Tue Feb 19 22:58:16
2013

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

2jzw: HOW THE HIV-1 NUCLEOCAPSID PROTEIN BINDS AND DESTABILISES THE (-)PRIMER BINDING SITE DURING REVERSE TRANSCRIPTION
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-200	2jzwA	28%	>target --SCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFARDCTSGGA- >2jzwA NVKCFNCGKEGHTARNCRAPR-----------------------KKGCWKCGKEGHQMKDCTERQAN [Model]
136-155	2jzwA	35%	>target ----------------------NSCFKCGEPGHMARECSQGG-- >2jzwA NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
180-198	2jzwA	42%	>target -LSCYSCGESGHFARDCTSG------------------------ >2jzwA NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]

2exf: SOLUTION STRUCTURE OF THE HIV-1 NUCLEOCAPSID (NCP7(12-55))COMPLEXED WITH THE DNA (-) PRIMER BINDING SITE
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-200	2exfA	28%	>target --SCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFARDCTSGGA- >2exfA NVKCFNCGKEGHTARNCRAPR-----------------------KKGCWKCGKEGHQMKDCTERQAN [Model]
136-155	2exfA	35%	>target ----------------------NSCFKCGEPGHMARECSQGG-- >2exfA NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
180-198	2exfA	42%	>target -LSCYSCGESGHFARDCTSG------------------------ >2exfA NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]

1aaf: NUCLEOCAPSID ZINC FINGERS DETECTED IN RETROVIRUSES: EXAFS INTACT VIRUSES AND THE SOLUTION-STATE STRUCTURE OF THE NUPROTEIN FROM HIV-1
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-200	1aafA	26%	>target -----------DNSCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFARDCTSGGA- >1aafA MQRGNFRNQRKIIKCFNCGKEGHIAKNCRAPR-----------------------KRGCWKCGKEGHQMKDCTERQAN [Model]
137-155	1aafA	37%	>target ----------------------------------SCFKCGEPGHMARECSQGG-- >1aafA MQRGNFRNQRKIIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTERQAN [Model]
178-198	1aafA	33%	>target ----------GGLSCYSCGESGHFARDCTSG------------------------ >1aafA MQRGNFRNQRKIIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTERQAN [Model]

1q3z: NMR STRUCTURE OF THE CYS28HIS MUTANT (E FORM) OF THE NUCLEOCAPSID PROTEIN NCP7 OF HIV-1.
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-198	1q3zA	26%	>target -SCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFARDCTSG- >1q3zA VKCFNCGKEGHTARNHRAPR-----------------------KKGCWKCGKEGHQMKDCTERQ [Model]
137-154	1q3zA	39%	>target ----------------------SCFKCGEPGHMARECSQG- >1q3zA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [Model]
181-198	1q3zA	39%	>target -SCYSCGESGHFARDCTSG---------------------- >1q3zA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [Model]
157-172	1q3zA	13%	>target -----------------------GYSGGGGGGRYGSGGG-- >1q3zA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [Model]

1q3y: NMR STRUCTURE OF THE CYS28HIS MUTANT (D FORM) OF THE NUCLEOCAPSID PROTEIN NCP7 OF HIV-1.
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-198	1q3yA	26%	>target -SCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFARDCTSG- >1q3yA VKCFNCGKEGHTARNHRAPR-----------------------KKGCWKCGKEGHQMKDCTERQ [Model]
137-154	1q3yA	39%	>target ----------------------SCFKCGEPGHMARECSQG- >1q3yA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [Model]
181-198	1q3yA	39%	>target -SCYSCGESGHFARDCTSG---------------------- >1q3yA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [Model]
157-172	1q3yA	13%	>target -----------------------GYSGGGGGGRYGSGGG-- >1q3yA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [Model]

1a1t: STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO THE SL3 PSI-RNA RECOGNITION ELEMENT, NMR, 25 STRUCTURES
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-200	1a1tA	26%	>target -----------DNSCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFARDCTSGGA- >1a1tA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPR-----------------------KKGCWKCGKEGHQMKDCTERQAN [Model]
137-154	1a1tA	39%	>target ----------------------------------SCFKCGEPGHMARECSQG--- >1a1tA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
178-198	1a1tA	33%	>target ----------GGLSCYSCGESGHFARDCTSG------------------------ >1a1tA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
157-172	1a1tA	13%	>target -----------------------------------GYSGGGGGGRYGSGGG---- >1a1tA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]

1f6u: NMR STRUCTURE OF THE HIV-1 NUCLEOCAPSID PROTEIN BOUND TO STEM-LOOP SL2 OF THE PSI-RNA PACKAGING SIGNAL. IMPLICATIONS FOR GENOME RECOGNITION
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-200	1f6uA	26%	>target -----------DNSCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFARDCTSGGA- >1f6uA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPR-----------------------KKGCWKCGKEGHQMKDCTERQAN [Model]
137-154	1f6uA	39%	>target ----------------------------------SCFKCGEPGHMARECSQG--- >1f6uA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
178-198	1f6uA	33%	>target ----------GGLSCYSCGESGHFARDCTSG------------------------ >1f6uA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
157-172	1f6uA	13%	>target -----------------------------------GYSGGGGGGRYGSGGG---- >1f6uA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]

1mfs: DYNAMICAL BEHAVIOR OF THE HIV-1 NUCLEOCAPSID PROTEIN; NMR,30 STRUCTURES
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

135-200	1mfsA	26%	>target -----------DNSCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFARDCTSGGA- >1mfsA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPR-----------------------KKGCWKCGKEGHQMKDCTERQAN [Model]
137-154	1mfsA	39%	>target ----------------------------------SCFKCGEPGHMARECSQG--- >1mfsA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
178-198	1mfsA	33%	>target ----------GGLSCYSCGESGHFARDCTSG------------------------ >1mfsA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
157-172	1mfsA	13%	>target -----------------------------------GYSGGGGGGRYGSGGG---- >1mfsA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]

2l4l: STRUCTURAL INSIGHTS INTO THE CTAR DNA RECOGNITION BY THE HNUCLEOCAPSID PROTEIN: ROLE OF SUGAR DEOXYRIBOSES IN THE BPOLARITY OF NC
Solved by: NMR, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

137-200	2l4lA	28%	>target ---SCFKCGEPGHMARECSQGGGGYSGGGGGGRYGSGGGGGGGGGGLSCYSCGESGHFARDCTSGGA- >2l4lA KNVKCFNCGKEGHTARNCRAP-----------------------RKKGCWKCGKEGHQMKDCTERQAN [Model]
136-155	2l4lA	35%	>target -----------------------NSCFKCGEPGHMARECSQGG-- >2l4lA KNVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
179-198	2l4lA	40%	>target -GLSCYSCGESGHFARDCTSG------------------------ >2l4lA KNVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
157-174	2l4lA	11%	>target -------------------------GYSGGGGGGRYGSGGGGG-- >2l4lA KNVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]

Downloads

download model.tgz

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.