SWISS-MODEL Repository - Model Details

Model Overview
Click on the bars to get more details about individual Models or experimental structures
1
220

Sequence
UniProt Q9FY50
Database: TrEMBL (Unreviewed) automatically annotated and not reviewed

STRING
Q9FY50: 3702.AT5G13510.1

Domain
Link to: [ InterPro ]
Ribosomal_L10

Model 3D Structure
Model information:
Modelled residue range: 71 to 198
Based on template: [ 3sgf ]  
Sequence Identity [%]: 29%
Model date: 2013-05-05
Revision date: 2013-04-01

Quaternary structure information: [details]
Template (3sgf): HETERO 14-mer
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                                        KGLTVKQF QDLRRTLPDT
3sgfH     1     malnlqdkqa ivaevsevak galsavvads --rgvtvdkm telrkagrea
                                                                      
TARGET                                                 hh    hhh      
3sgfH              hhhhhhh hhhhh   h    sssss          hh    hhh      


TARGET    19    TK-LIVAKNT LVFKAIEGTK WEALKPCMKG MNAWLFVQTD EIPSA-IKPY
3sgfH     49    gvymrvvrnt llrravegtp feclkdafvg pt--liaysm ehpgaaarlf
                                                                      
TARGET                                                              hh
3sgfH                          hhh                     ssss s       hh


TARGET    67    RSFQKERKLE NNDFAGAVFE GKFYAPDNFK VLETMPTRAE VYAKMLGAL-
3sgfH     97    kefakana-- kfevkaaafe gelipasqid rlatlptyee aiarlmatmk
                                                                      
TARGET          hhhhhh                                       hhhhhh   
3sgfH           hhhhhhhh                                        hhh   


TARGET    116   QSPAINLVTT LQA -----                                  
3sgfH     145   easagklvrt laavrdake                                  
                                                                      
TARGET            h                                                   
3sgfH

Quality 


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

 
Quaternary Structure Annotation of the Template 
 3sgf is annotated as HETERO 14-mer 
 PISA was used to annotate the quaternary structure, because the author assignment was 
  The template was built based on the following PISA annotation file: 3sgf_assembly.xml.gz 
      
 
Quaternary Structure Modelling of the Target Protein 
 3sgf_1

Template Selection 
 - Start SMR-Pipeline for:a93d44d8d026b653db28b8869c9c59a7 on BC2-cluster at Sun May  5 12:23:29
2013 


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

 - Run HHSearch to detect more templates...
FATAL - No md5 found in hash for: 3j37J
FATAL - No md5 found in hash for: 3j37J
 - Generate new template library
 - Run template selection against modified template library 
 - Summarize templates: 
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with G found
 - No template with F found
 - No template with I found
 - No template with S found
 - No template with O found
 - No template with L found
 - No template with Q found
 - No template with 3 found
 - No template with 2 found
 - No template with 5 found
 - No template with T found
 - No template with X found
 - No template with V found
 - No template with 8 found
 - No template with Z found
 - No template with U found
 - No template with G found
 - No template with F found
 - No template with I found
 - No template with S found
 - No template with O found
 - No template with L found
 - No template with Q found
 - No template with 3 found
 - No template with 2 found
 - No template with 5 found
 - No template with T found
 - No template with X found
 - No template with V found
 - No template with 8 found
 - No template with Z found
 - No template with U found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z found
 - No template with U found
 - No template with V found
 - No template with W found
 - No template with X found
 - No template with Y found
 - No template with Z 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 F found
 - No template with I found
 - No template with S found
 - No template with O found
 - No template with 3 found
 - No template with 2 found
 - No template with 5 found
 - No template with T found
 - No template with V found
 - No template with 8 found
 - No template with Z found
 - No template with U found
 - No template with G found
 - No template with F found
 - No template with I found
 - No template with S found
 - No template with O found
 - No template with 3 found
 - No template with 2 found
 - No template with 5 found
 - No template with T found
 - No template with V found
 - No template with 8 found
 - No template with Z found
 - No template with U found
 - Proof template(s) selection compared to previous Repository update
 - Different number of templates selected (old0 vs new:2): model based on new templates
 - Send 2 Templates for modeling

 - @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
 -                           ***********************************************
 - building model based on 3sgfH (71-198) was successful 
 -                 **************************************************************
 - building model based on 1zavA (43-213) 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:a93d44d8d026b653db28b8869c9c59a7 on BC2-cluster at Sun May  5 12:29:17
2013


Template Description
Match Chain SeqId

3kir: STRUCTURE OF RELE NUCLEASE BOUND TO THE 70S RIBOSOME (PRECLEAVAGE STATE; PART 2 OF 4)
Solved by: X-RAY, Resolution: 3.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

46-176 3kirJ 26%
[Model]

1zav: RIBOSOMAL PROTEIN L10-L12(NTD) COMPLEX, SPACE GROUP P21
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

41-214 1zavA 26%
[Model]

1zaw: RIBOSOMAL PROTEIN L10-L12(NTD) COMPLEX, SPACE GROUP P21212FORM A
Solved by: X-RAY, Resolution: 2.30A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

41-214 1zawA 26%
[Model]

3kiy: STRUCTURE OF RELE NUCLEASE BOUND TO THE 70S RIBOSOME (POSTCLEAVAGE STATE; PART 4 OF 4)
Solved by: X-RAY, Resolution: 3.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

46-176 3kiyJ 26%
[Model]

3kit: STRUCTURE OF RELE NUCLEASE BOUND TO THE 70S RIBOSOME (PRECLEAVAGE STATE; PART 4 OF 4)
Solved by: X-RAY, Resolution: 3.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

46-176 3kitJ 26%
[Model]

3kiw: STRUCTURE OF RELE NUCLEASE BOUND TO THE 70S RIBOSOME (POSTCLEAVAGE STATE; PART 2 OF 4)
Solved by: X-RAY, Resolution: 3.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

46-176 3kiwJ 26%
[Model]

1zax: RIBOSOMAL PROTEIN L10-L12(NTD) COMPLEX, SPACE GROUP P21212FORM B
Solved by: X-RAY, Resolution: 2.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

45-214 1zaxA 26%
[Model]

3i8i: ELONGATION COMPLEX OF THE 70S RIBOSOME WITH THREE TRNAS ANMRNA. THIS ENTRY 3I8I CONTAINS 50S RIBOSOMAL SUBNIT. THE 30S RIBOSOMAL SUBUNIT CAN BE FOUND IN PDB ENTRY 3I8H. MOLECULE A IN THE SAME ASYMMETRIC UNIT IS DEPOSITED AS 3I(50S) AND 3I8G (30S).
Solved by: X-RAY, Resolution: 3.10A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

43-188 3i8iY 26%
[Model]

3sgf: CRYSTAL STRUCTURE OF RELEASE FACTOR RF3 TRAPPED IN THE GTPROTATED CONFORMATION OF THE RIBOSOME
Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

41-215 3sgfH 22%
[Model]

3uos: CRYSTAL STRUCTURE OF RELEASE FACTOR RF3 TRAPPED IN THE GTPROTATED CONFORMATION OF THE RIBOSOME (WITHOUT VIOMYCIN)
Solved by: X-RAY, Resolution: 3.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

41-215 3uosH 22%
[Model]

3jyw: STRUCTURE OF THE 60S PROTEINS FOR EUKARYOTIC RIBOSOME BASEON CRYO-EM MAP OF THERMOMYCES LANUGINOSUS RIBOSOME AT 8.9RESOLUTION
Solved by: X-RAY, Resolution: 8.90A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

44-155 3jyw8 21%
[Model]

3j0y: STRUCTURAL CHARACTERIZATION OF MRNA-TRNA TRANSLOCATION INT(50S RIBOSOME OF CLASS 4B OF THE SIX CLASSES)
Solved by: X-RAY, Resolution: 14.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

42-217 3j0yJ 21%
[Model]

3j0w: STRUCTURAL CHARACTERIZATION OF MRNA-TRNA TRANSLOCATION INT(50S RIBOSOME OF CLASS 4A OF THE SIX CLASSES)
Solved by: X-RAY, Resolution: 14.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

42-217 3j0wJ 21%
[Model]

3j11: STRUCTURAL CHARACTERIZATION OF MRNA-TRNA TRANSLOCATION INT(50S RIBOSOME OF CLASS 3 OF THE SIX CLASSES)
Solved by: X-RAY, Resolution: 14.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

42-217 3j11J 21%
[Model]

3j14: STRUCTURAL CHARACTERIZATION OF MRNA-TRNA TRANSLOCATION INT(50S RIBOSOME OF CLASS 6 OF THE SIX CLASSES)
Solved by: X-RAY, Resolution: 14.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

42-217 3j14J 21%
[Model]

3j0t: STRUCTURAL CHARACTERIZATION OF MRNA-TRNA TRANSLOCATION INT(50S RIBOSOME OF CLASS2 OF THE SIX CLASSES)
Solved by: X-RAY, Resolution: 14.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

42-217 3j0tJ 21%
[Model]

3j12: STRUCTURAL CHARACTERIZATION OF MRNA-TRNA TRANSLOCATION INT(50S RIBOSOME OF CLASS 5 OF THE SIX CLASSES)
Solved by: X-RAY, Resolution: 14.70A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

42-217 3j12J 21%
[Model]

3jsy: N-TERMINAL FRAGMENT OF RIBOSOMAL PROTEIN L10 FROM METHANOCJANNASCHII
Solved by: X-RAY, Resolution: 1.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

46-139 3jsyA 20%
[Model]
46-140 3jsyB 20%
[Model]

2qa4: A MORE COMPLETE STRUCTURE OF THE THE L7/L12 STALK OF THE HALOARCULA MARISMORTUI 50S LARGE RIBOSOMAL SUBUNIT
Solved by: X-RAY, Resolution: 3.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

44-161 2qa4G 20%
[Model]

3o5h: YEAST 80S RIBOSOME. THIS ENTRY CONSISTS OF THE 60S SUBUNITSECOND 80S IN THE ASYMMETRIC UNIT.
Solved by: X-RAY, Resolution: 4.00A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

45-165 3o5hM 20%
[Model]

3a1y: THE STRUCTURE OF PROTEIN COMPLEX
Solved by: X-RAY, Resolution: 2.13A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

41-186 3a1yG 17%
[Model]

3j21: PROMISCUOUS BEHAVIOR OF PROTEINS IN ARCHAEAL RIBOSOMES REVCRYO-EM: IMPLICATIONS FOR EVOLUTION OF EUKARYOTIC RIBOSOMRIBOSOMAL PROTEINS)
Solved by: X-RAY, Resolution: 6.60A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

46-156 3j21k 15%
[Model]

3izr: LOCALIZATION OF THE LARGE SUBUNIT RIBOSOMAL PROTEINS INTO CRYO-EM MAP OF TRITICUM AESTIVUM TRANSLATING 80S RIBOSOME
Solved by: X-RAY, Resolution: 5.50A, Identified by HHSEARCH
[ SMTL ]   [ RCSB ]   [ PDBe ]   [ SCOP ]  [ CATH ]  

45-187 3izrs 9%
[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.