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Model Overview

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1268

Sequence

UniProt

Q09575

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

Domain

Link to: [ InterPro ]

	RVT_1
	rve
	Asp_protease_2

Model 3D Structure

	Model information:
	Modelled residue range:	845 to 954
	Based on template:	[ 2x78 ]
	Sequence Identity [%]:	33%
	Model date:	2013-02-20
	Revision date:	2013-01-30

Quaternary structure information:	[details]
Template (2x78): DIMER 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     PEAPWKRIHI DFAGPLNG-- --CYLLVVVD AKTKYAEVKL TRSISAVTTI
2x78C     118   pqkpfdkffi dyigplppsq gylyvlvvvd gmtgftwlyp tkapstsatv
                                                                      
TARGET               sssss sss           sssssss s   ssssss s    hhhhh
2x78C                sssss sss           sssssss s   ssssss s    hhhhh


TARGET    47    DLLEEIFSIH GYPETIISDN GTQLTSHLFA QMCQSHGI-- EHKTSAVYYP
2x78C     168   kslnvltsi- aiprvihsdq gaaftsstfa ewakergihl efstsgskve
                                                                      
TARGET          hhhhhhh        sss     hhh   hhh hh                hhh
2x78C           hhhhh         sssss    hh   hhhh hhhhhh  ss sss    hhh


TARGET    95    RSNGAAERFV DTLKRG --- ---------- ---------- ----------
2x78C     222   rknsdikrll tkllvgrptk wydllpvvql alnntyspvl kytphqllfg
                                                                      
TARGET          hhhhhhhhhh hhh                                        
2x78C           hhhhhhhhhh hhh         h   hhhhh hhh           hhhhhh 


TARGET          ---------- ---------- ---------- ----                 
2x78C     272   idsntpfanq dtldltreee lsllqeirts lyhp                 
                                                                      
TARGET                                                                
2x78C                             hhh hhhhhhhhhh hh

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 
 2x78 is annotated as DIMER 
 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: 2x78.pdb2.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 The target and template sequences are too diverse (seqid: 33.621) to infer a conservation of the oligomeric state 
 Please use the advancend features of the SwissModel Project Mode 
       
 The target structure was calculated as SINGLE CHAIN

Template Selection

 - Start SMR-Pipeline for:f8e6a764cac123de41b36854a9578e1f on BC2-cluster at Wed Feb 20 15:18:38
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: 
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 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:7): model based on new templates
 - Send 7 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                                                      *******
 - building model based on 2x78C (845-954) was successful 
 -                                                      **********
 - building model based on 3oymB (845-995) was successful 
 -                                                  ************
 - building model based on 4be2A (775-958) was successful 
 -                                                  **************
 - building model based on 3s3nA (775-995) was successful 
 -                              ***********
 - building model based on 3qlhB (452-623) was successful 
 -                           *****************
 - building model based on 1rw3A (412-677) was not successful go to next best template
 -                           ***************
 - building model based on 1ztwA (412-649) was successful 
 -               **
 - building model based on 1aafA (224-258) 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:f8e6a764cac123de41b36854a9578e1f on BC2-cluster at Wed Feb 20 15:23:00
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 ]

	224-258	2jzwA	15%	>target -KPEKSSQDS-KKKGEIP-----TCFYCNKKGHYATNCRSNP-- >2jzwA NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
	240-258	2jzwA	53%	>target --TCFYCNKKGHYATNCRSNP----------------------- >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 ]

	224-258	2exfA	15%	>target -KPEKSSQDS-KKKGEIP-----TCFYCNKKGHYATNCRSNP-- >2exfA NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
	240-258	2exfA	53%	>target --TCFYCNKKGHYATNCRSNP----------------------- >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 ]

	224-258	1aafA	15%	>target ------------KPEKSSQDS-KKKGEIP-----TCFYCNKKGHYATNCRSNP-- >1aafA MQRGNFRNQRKIIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTERQAN [Model]
	238-258	1aafA	52%	>target -----------IPTCFYCNKKGHYATNCRSNP----------------------- >1aafA MQRGNFRNQRKIIKCFNCGKEGHIAKNCRAPRKRGCWKCGKEGHQMKDCTERQAN [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 ]

	224-258	1f6uA	15%	>target ------------KPEKSSQDS-KKKGEIP-----TCFYCNKKGHYATNCRSNP-- >1f6uA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
	239-258	1f6uA	50%	>target ------------PTCFYCNKKGHYATNCRSNP----------------------- >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 ]

	224-258	1mfsA	15%	>target ------------KPEKSSQDS-KKKGEIP-----TCFYCNKKGHYATNCRSNP-- >1mfsA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
	239-258	1mfsA	50%	>target ------------PTCFYCNKKGHYATNCRSNP----------------------- >1mfsA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [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 ]

	224-258	1a1tA	15%	>target ------------KPEKSSQDS-KKKGEIP-----TCFYCNKKGHYATNCRSNP-- >1a1tA MQKGNFRNQRKTVKCFNCGKEGHIAKNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
	239-258	1a1tA	50%	>target ------------PTCFYCNKKGHYATNCRSNP----------------------- >1a1tA 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 ]

	224-258	2l4lA	15%	>target --KPEKSSQDS-KKKGEIP-----TCFYCNKKGHYATNCRSNP-- >2l4lA KNVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [Model]
	239-258	2l4lA	50%	>target --PTCFYCNKKGHYATNCRSNP----------------------- >2l4lA KNVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTERQAN [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 ]

	225-258	1q3yA	15%	>target -PEKSSQDS-KKKGEIP-----TCFYCNKKGHYATNCRSNP >1q3yA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [Model]
	240-258	1q3yA	47%	>target -TCFYCNKKGHYATNCRSNP--------------------- >1q3yA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [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 ]

	225-258	1q3zA	15%	>target -PEKSSQDS-KKKGEIP-----TCFYCNKKGHYATNCRSNP >1q3zA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [Model]
	240-258	1q3zA	47%	>target -TCFYCNKKGHYATNCRSNP--------------------- >1q3zA VKCFNCGKEGHTARNHRAPRKKGCWKCGKEGHQMKDCTERQ [Model]

4fcy: CRYSTAL STRUCTURE OF THE BACTERIOPHAGE MU TRANSPOSOSOME
Solved by: X-RAY, Resolution: 3.71A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	847-993	4fcyB	11%	>target --------------------------------------------------------------------------------------------------------------------------------------------------APWKRIHIDFA----------GPLNGCYLLVVVDAKTKYAEVKLT-RSISAVTTIDLLEEIFSIHGYPE--TIISDNGTQLTSHLF-----------------AQMCQSHGIEHKTSAVYYPRSNGA---AERFVDT--LKRGIAKI-------KGEG--S--VNQQ---ILNKFLISYRNTPHSALNG----STPAECH---------------------------------------------------------------------------------------------------------------------------------- >4fcyB DREALWSKWDNASDSQRRLAEKWLPAVQAADEMLNQGISTKTAFATVAGHYQVSASTLRDKYYQVQKFAKPDWAAALVSEFDEDAWQFLIADYLRPEKPAFRKCYERLELAAREHGWSIPSRATAFRRIQQLDEAMVVACREGEHLDAMQWINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTRKILGWRCDVSENIDSIRLSFMDVVTRYGIPEDFHITIDNTRGAANKWLTGGAPNRYRFKVKEDDPKGLFLLMGAKMHWTSVVAGKGWGQAKPVERAFGVGGLEEYVDKHPALAGAYTGPYGDRAVDAELFLKTLAEGVAMFNARTGRETEMCGGKLSFDDVFEREYARTIVRKPTEEQKRMLLLPAEAVNVSRKGEFTLKVGGSLKGAKNVYYNLALMLAGVKKVVVRFDPQQLHSTVYCYTLDGRFICEAECLAAAGREYRRRQKQLKSATKAAIKAQKQMDALEVAELLP [Model]
	848-995	4fcyA	13%	>target --------------------------------------------------------------------------------------------------------------------------------------------------------PWKRIHIDF-----A-----GPLNGCYLLVVVDAKTKYAEVKLT-RSISAVTTIDLLEEIFSIHGYPET--IISDNGTQLTSHLFAQ---------MCQSHGIEHKTSAVYYPRSNGAAERFVDTLKRGIAKI---KGEGSVNQQI---LNKFLISYRNTPHSALN---GSTPAECHFG------------------------------------------------------------------------------------------------------------------ >4fcyA DREALWSKWDNASDSQRRLAEKWLPAVQAADEMLNQGISTKTAFATVAGHYQVSASTLRDKYYQVQKFAKPDWAAALVSEFDEDAWQFLIADYLRPEKPAFRKCYERLELAAREHGWSIPSRATAFRRIQQLDEAMVVACREGEHALMEHLDAMQWINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTRKILGWRCDVSENIDSIRLSFMDVVTRYGIPEDFHITIDNTTGGAPNRYRFKVKEDDPKGLFLLMGAKMHWLEEYVDKHPALAGAY--TGPNPQAKPDNYGDRAVDAELFLKTLAEGVAMFNARTGRETEMCGGKLSFDDVFEREYARTIVRKPTEEQKRMLLLPAEAVNVSRKGEFTLKVGGSLKGAKNVYYNLALMLAGVKKVVVRFDPQQLHSTVYCYTLDGRFICEAECLREYRRRQKQLKSATKAAIKAQKQ [Model]

1bco: BACTERIOPHAGE MU TRANSPOSASE CORE DOMAIN
Solved by: X-RAY, Resolution: 2.40A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

858-994

1bcoA

10%

[Model]

1bcm: BACTERIOPHAGE MU TRANSPOSASE CORE DOMAIN WITH 2 MONOMERS PER ASYMMETRIC UNIT
Solved by: X-RAY, Resolution: 2.80A, Identified by HHSEARCH
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

	863-994	1bcmB	9%	>target -----------------------------CYLLVVVDAKTKYAEVKLT-RSISAVTTIDLLEEIFSIHGYPET--IISDNGTQLTSHLF-----------------AQMCQSHGIEHKTSAVYYPRSNGA---AERFVDTLK--RGIAKIKG-------EG---------------SVNQQILNKFLISYRNTPHSAL----NGSTPAECHF------------------------------------------------------------------------------------------- >1bcmB EHLDAMQWINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTRKILGWRCDVSENIDSIRLSFMDVVTRYGIPEDFHITIDNTRGAANKWLTGGAPNRYRFKVKEDDPKGLFLLMGAKMHWTSVVAGKGWGQAKPVERAFGVGGLEEYVDKHPALAGAYTGPNPQAKPDNYGDRAVDAELFLKTLAEGVAMFNARTGRETEMCGGKLSFDDVFEREYARTIVRKPTEEQKRMLLLPAEAVNVSRKGEFTLKVGGSLKGAKNVYYNMALMNAGVKKVVVRFDPQQLHSTVYCYTLDGRFICEAECL [Model]
	863-994	1bcmA	10%	>target ------------------------------CYLLVVVDAKTKYAEVKLTR-SISAVTTIDLLEEIFSIHGYPET--IISDNGTQLTSHLF-----------------AQMCQSHGIEHKTSAVYYPRSNGA---AERFVDTLK--RGIAKIKG---E--G-----------------SVNQQILNKFLISYRNTPHSAL----NGSTPAECHF------------------------------------------------------------------------------------------- >1bcmA VEHLDAMQWINGDGYLHNVFVRWFNGDVIRPKTWFWQDVKTRKILGWRCDVSENIDSIRLSFMDVVTRYGIPEDFHITIDNTRGAANKWLTGGAPNRYRFKVKEDDPKGLFLLMGAKMHWTSVVAGKGWGQAKPVERAFGVGGLEEYVDKHPALAGAYTGPNPQAKPDNYGDRAVDAELFLKTLAEGVAMFNARTGRETEMCGGKLSFDDVFEREYARTIVRKPTEEQKRMLLLPAEAVNVSRKGEFTLKVGGSLKGAKNVYYNMALMNAGVKKVVVRFDPQQLHSTVYCYTLDGRFICEAECL [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.