SWISS-MODEL Repository - Model Details

Model Overview
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1
995

Sequence
UniProt Q8N5C6
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q8N5C6: 9606.ENSP0000026

Domain
Link to: [ InterPro ]
S1
Tex_N
HHH_3

Model 3D Structure
Model information:
Modelled residue range: 224 to 991
Based on template: [ 3bzc ]  
Sequence Identity [%]: 33%
Model date: 2013-04-22
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (3bzc): 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 ]

Alignment 

TARGET    1                            IEPWVCANI IRLFNDDNTI PFIIRYRKEL
3bzcA     1     mdsintriae elsalpsgr- -vqpqqvaaa valldegstv pfiaryrkev
                                                                      
TARGET                                    hhhhhh hhhhh    h hhhhh   hh
3bzcA            hhhhhhhhh hhh            hhhhhh hhhhh    h hhhhh   hh


TARGET    30    INNLDADSLR EVQQTLEELR AVAKKVHSTI QKIKKEGKMS ECLLKAMLNC
3bzcA     49    tgslddtqlr mleerlrylr eleerrgail asieeqgklt pelardikla
                                                                      
TARGET          h    hhhhh hhhhhhhhhh hhhhhhhhhh hhhhh      hhhhhhhhh 
3bzcA           h    hhhhh hhhhhhhhhh hhhhhhhhhh hhhhh      hhhhhhhhh 


TARGET    80    KTFEELEHVS APYKTGSKGT KAQRARQLGL EGAARALLEK PGELS---LL
3bzcA     99    dtktrledly lpykqkrr-t kgqialeagl galadalfdd ptlvpeseaa
                                                                      
TARGET            hhhhhhhh h           hhhhh   h hhhhhhhhh            
3bzcA             hhhhhhhh h          hhhhhh   h hhhhhhhhh      hhhhhh


TARGET    127   SYIRPDVKGL STLQDIEIGV QHILADMIAK DKDTLDFIRN LCQKRHVCIQ
3bzcA     148   rfvdae-kgf advkavlega kyilmerfae datlldklrv fmkne----a
                                                                      
TARGET                       hhhhhhhh hhhhhhhh    hhhhhhhhh hhh       
3bzcA           h            hhhhhhhh hhhhhhhh    hhhhhhhhh hhhhh    s


TARGET    177   SSLAKVSSKK VNEKDVDKFL LYQHFSCNIR NIHHHQILAI NRGENLKVLT
3bzcA     193   tltarvvpgk --eqegakfs dyfehdeplk sapshralai frgrnegvls
                                                                      
TARGET          sssssss                 sssss       hhhhhhh h      sss
3bzcA           sssssss                 sssssss     hhhhhhh h      sss


TARGET    227   VKVNISDGVK DEFC--RWCI QNRWRPRSFA RPELMKILYN SLNDSFKRLI
3bzcA     241   aslkvgeeap gtlhpcevmi aerfglsnqg raa-dkwlae vvrwtwkvkl
                                                                      
TARGET          ssss               hh hhh              hhhh hhhhhhhhhh
3bzcA           ssss           hhhhhh hhh          h hhhhhh hhhhhhhhhh


TARGET    275   YPLLCREFRA KLTSDAEKES VMMFGRNLRQ LLLTSPVPGR TLMGVDPGYK
3bzcA     290   ythletdlfg elrdgaedea isvfarnlhd lllaapagpr atlgldpglr
                                                                      
TARGET          hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hh          sssss    
3bzcA           hhhhhhhhhh hhhhhhhhhh hhhhhhhhhh hhh         sssss    


TARGET    325   HGCKLAIISP TSQILHTDVV YLHC--GQGF REAEKIKTLL LNFNCSTVVI
3bzcA     340   tgvkvavvda tgklldtatv yphapknqwd qtlavlaalc akhqveliai
                                                                      
TARGET            sssssss    ssssssss         hh hhhhhhhhhh hhh  sssss
3bzcA             sssssss    ssssssss         hh hhhhhhhhhh hhh  sssss


TARGET    373   GNGTACRETE AYFADLIMKN YFAPLDVVYC IVSEAGASIY SVSPEANKEM
3bzcA     390   gngtasretd klagelikk- -ypgmkltki mvseagasvy saselaakef
                                                                      
TARGET          ss   hhhhh hhhhhhhh          sss ss  hhhhhh h   hhhhh 
3bzcA           ss   hhhhh hhhhhhhhh         sss ss  hhhhhh    hhhhhh 


TARGET    423   PGLDPNLRSA VSIARRVQDP LAELVKIEPK HIGVGMYQHD VSQTLLKATL
3bzcA     438   peldvslrga vsiarrlqdp laelvkiepk sigvgqyqhd vsqlklarsl
                                                                      
TARGET               hhhhh hhhhhhh    hhhhh   hh h            hhhhhhhh
3bzcA                hhhhh hhhhhhh    hhhhh   hh h            hhhhhhhh


TARGET    473   DSVVEECVSF VGVDINICSE VLLRHIAGLN ANRAKNIIEW REKNGPFINR
3bzcA     488   davvedcvna vgvdvntasa allarisgln stlaqnivah rdangafrtr
                                                                      
TARGET          hhhhhhhhhh h        h hhhh       hhhhhhhhhh hhh       
3bzcA           hhhhhhhhhh h        h hhhh       hhhhhhhhhh hhh       


TARGET    523   EQLKKVKGLG PKSFQQCAGF IRIN-QDYIR TFCSQQTETS GQIQGVAVTS
3bzcA     538   delkkvsrlg ektfeqaagf lrvmngdnpl dasavhpety plvqriaadt
                                                                      
TARGET          hhhh       hhhhhhhhhh          h h        h hhhhhhhhhh
3bzcA           hhhh       hhhhhhhhhh          h h        h hhhhhhhhhh


TARGET    572   SADVEVTNEK QGKKKSKTAV NVLLKPNPLD QTCIHPESYD IAMRFLSSIG
3bzcA     588   erdi------ ----rsligd saflkr---- ---ldpkkft detfglptvt
                                                                      
TARGET             sss      sss       hhh   hhh                  hhhhh
3bzcA              h           hhh    hhhhhh                     hhhhh


TARGET    622   GTLYEVGKPE MQQKINSFLE KEGMEKIAER LQTTVHTLQV IIDGLSQPES
3bzcA     621   dilkeldkp- ---------- ---------- ---------- ---------g
                                                                      
TARGET          hhhhhhh  s ssss    hh hhh                      ssssss 
3bzcA           hhhhhhh                                               


TARGET    672   FDFRTDFDKP DFKRSIVCLE DLQIGTVLTG KVENATLFGI FVDIGVGKSG
3bzcA     631   rdprpefkta efqegveslk dlkpgmvleg vvtnvtnfga fvdigvhqdg
                                                                      
TARGET                                     sssss ssssss sss sss      s
3bzcA                                      sssss ssssss sss sss      s


TARGET    722   LIPIRNVTEA KLSKTKKRRS LGLGPGERVE VQVLNIDIPR SRITLDL --
3bzcA     681   lvhisalse- ---kfvkdpy evvkagdivk vkvmevdipr nrvglsmrms
                                                                      
TARGET          sssshh              h hh    ssss ssssssss   ssssss    
3bzcA           ssss                h hh    ssss sss ssss   ssss      


TARGET          ----                                                  
3bzcA     727   dtpg                                                  
                                                                      
TARGET                                                                
3bzcA

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3bzc 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: 3bzc.pdb1.gz 
      
 
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 0.2 (>0.5 indicates similarity)

Template Selection 
 - Start SMR-Pipeline for:c7041055b45003e112c850ffb0d1432e on BC2-cluster at Sun Apr 21 22:22:42
2013 


 - Analyze BLAST summary ... 
 - No templates found with BLAST (seqid-cutoff: 60): go to HHSEARCH

 - No A3m found

 - Run HHSearch to detect more templates...
 - Generate new template library
 - Run template selection against modfied template library 
 - Summarize templates: 
 - No template with A found
 - No template with B found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with E found
 - No template with F found
 - No template with G found
 - No template with H found
 - No template with K 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

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                   **************************************************************
 - building model based on 3bzcA (224-991) 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:c7041055b45003e112c850ffb0d1432e on BC2-cluster at Sun Apr 21 22:28:47
2013


Template Description
Match Chain SeqId

2vnu: CRYSTAL STRUCTURE OF SC RRP44
Solved by: X-RAY, Resolution: 2.3A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

918-983 2vnuD 23%
[Model]

2wp8: YEAST RRP44 NUCLEASE
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

919-991 2wp8J 22%
[Model]

4ifd: CRYSTAL STRUCTURE OF AN 11-SUBUNIT EUKARYOTIC EXOSOME COMPRNA
Solved by: X-RAY, Resolution: 2.81A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

919-992 4ifdJ 23%
[Model]
916-991 4ifdI 17%
[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.