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Model Overview

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508

Sequence

UniProt

O44081

Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING

O44081: 7227.FBpp0072166

Domain

Link to: [ InterPro ]

	PUA
	TruB_N
	DKCLD

Model 3D Structure

	Model information:
	Modelled residue range:	46 to 406
	Based on template:	[ 3uai ]
	Sequence Identity [%]:	70%
	Model date:	2013-02-21
	Revision date:	2013-01-30

Quaternary structure information:	[details]
Template (3uai): HETERO TETRAMER 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       DTSQWPLL LKNFDKLNIR SNHYTPLAHG SSPLNRDIKE YMKTGFINLD
3uaiA     18      dtsewpll lknfdkllvr sghytpipag ssplkrdlks yissgvinld
                                                                      
TARGET                            sss                   hhh hhssssssss
3uaiA                             sss                   hhh hhssssssss


TARGET    49    KPSNPSSHEV VAWIKKILKV EKTGHSGTLD PKVTGCLIVC IDRATRLVKS
3uaiA     66    kpsnpsshev vawikrilrc ektghsgtld pkvtgclivc idratrlvks
                                                                      
TARGET          s     hhhh hhhhhhhh    sssss        sssssss ssshh   hh
3uaiA           s     hhhh hhhhhhhh    sssss         ssssss ssshh   hh


TARGET    99    QQSAGKEYVA IFKLHGAVES VAKVRQGLEK LRGALFQRPP LISAVKRQLR
3uaiA     116   qqgagkeyvc ivrlhdalkd ekdlgrslen ltgalfqrpp l----krqlr
                                                                      
TARGET          hhh ssssss sssss       hhhhhhhhh   sssss             s
3uaiA           hhh ssssss sssss       hhhhhhhhh   sssss             s


TARGET    149   VRTVYDSKLL DYDETRNMGV FWVSCEAGSY IRTMCVHLGL VLGVGGQMLE
3uaiA     166   vrtiyesnli efdnkrnlgv fwasceagty mrtlcvhlgm llgvgghmqe
                                                                      
TARGET          ssssssssss ssss  ssss ssssss     hhhhhhhhhh hh  ssssss
3uaiA           ssssssssss ssss  ssss ssssss     hhhhhhhhhh h   ssssss


TARGET    199   LRRVRSGIQS ERDGMVTMHD VLDAMWLYEN HKDESMLRRV IKPLEGLLVN
3uaiA     216   lrrvrsgals endnmvtlhd vmdaqwvydn trdesylrsi iqpletllvg
                                                                      
TARGET          sssssss ss s      hhh hhhhhhhhh      hhh     ssshh    
3uaiA           sssssss ss s      hhh hhhhhhhhh      hhhh    ssshh    


TARGET    249   HKRIIMKDSS VNAVCYGAKI TLPGVLRYED GIEIDQEIVI CTTKGEAICL
3uaiA     266   ykrivvkdsa vnavcygakl mipgllryee gielydeivl ittkgeaiav
                                                                      
TARGET           ssssssh    hhhhh   s ss ssssss       sssss ss   sssss
3uaiA            sssss h    hhhhh   s ss   ssss       sssss ss   sssss


TARGET    299   AIALMTTATM ASCDHGVVAK IKRVIMERDT YPRKWGLGPK ASAKKALIAA
3uaiA     316   aiaqmstvdl ascdhgvvas vkrcimerdl yprrwglgpv aqkkkqmkad
                                                                      
TARGET          ssss  hhhh hh   sssss sssss               h hhhhhhhhh 
3uaiA           ssss  hhhh hh   sssss sssss               h hhhhhhhh  


TARGET    349   GKLDKFGRPN ENT                                        
3uaiA     366   gkldkygrvn ent-                                       
                                                                      
TARGET                                                                
3uaiA

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
3uai is annotated as HETERO TETRAMER
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: 3uai.pdb1.gz

Quaternary Structure Modelling of the Target Protein
3uai_1

Template Selection

 - Start SMR-Pipeline for:e11e7d81745512068d7be9dddda65d2a on BC2-cluster at Thu Feb 21 14:05:37
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

FATAL - No A3m found

 - Run HHSearch to detect more templates...
FATAL - No templates found in HHSEARCH, strange
 - No template with D found
 - No template with F found
 - No template with C found
 - No template with E found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with C found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with D found
 - No template with B found
 - No template with B found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C found
 - No template with D found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with D found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with C found
 - No template with A found
 - No template with B found
 - No template with D found
 - No template with B found
 - No template with C found
 - No template with B found
 - No template with C 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 3uaiA (46-406) 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:e11e7d81745512068d7be9dddda65d2a on BC2-cluster at Thu Feb 21 14:07:37
2013

Template Search

[ start new template identification in Workspace ]

Template Description

Match

Chain

SeqId

3uai: STRUCTURE OF THE SHQ1-CBF5-NOP10-GAR1 COMPLEX FROM SACCHARCEREVISIAE
Solved by: X-RAY, Resolution: 3.06A, Identified by BLAST
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

46-406

3uaiA

70%

[Model]

3zv0: STRUCTURE OF THE SHQ1P-CBF5P COMPLEX
Solved by: X-RAY, Resolution: 2.80A, Identified by BLAST
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

265-405	3zv0D	60%	>target ----------LDAMWLYENHKDESMLRRVIK------PLEGLLVNHKRIIMKDSSVNAVCYGAKITLPGVLRYEDGIEIDQEIVICTTKGEAICLAIALMTTATMASCDHGVVAKIKRVIMERDTYPRKWGLGPKASAKKALIAAGKLDKFGRPNEN >3zv0D TSEWPLLLKNFDKLLVRSGHYTPIPLKRDLKSYISSGPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRWGLGPVAQKKKQMKADGKLDKYGRVNEN [Model]
286-405	3zv0C	69%	>target --------------------------------PLEGLLVNHKRIIMKDSSVNAVCYGAKITLPGVLRYEDGIEIDQEIVICTTKGEAICLAIALMTTATMASCDHGVVAKIKRVIMERDTYPRKWGLGPKASAKKALIAAGKLDKFGRPNEN >3zv0C SEWPLLLKNFDKLLVRSGSPLKRDLKSYISSGPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRWGLGPVAQKKKQMKADGKLDKYGRVNEN [Model]
47-88	3zv0D	62%	>target TSQWPLLLKNFDKLNIRSNHYTPLAHGSSPLNRDIKEYMKTG------------------------------------------------------------------------------------------------------------------------ >3zv0D TSEWPLLLKNFDKLLVRSGHYTPI-----PLKRDLKSYISSGPLETLLVGYKRIVVKDSAVNAVCYGAKLMIPGLLRYEEGIELYDEIVLITTKGEAIAVAIAQMSTVDLASCDHGVVASVKRCIMERDLYPRRWGLGPVAQKKKQMKADGKLDKYGRVNEN [Model]

3u28: CRYSTAL STRUCTURE OF A CBF5-NOP10-GAR1 COMPLEX FROM SACCHACEREVISIAE
Solved by: X-RAY, Resolution: 1.90A, Identified by BLAST
[ SMTL ] [ RCSB ] [ PDBe ] [ SCOP ] [ CATH ]

33-378

3u28A

69%

[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.