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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST TSR1, A PRE-40S RIBOSOME SYNTHESIS FACTOR
 
Authors :  U. M. Mccaughan, U. Jayachandran, A. G. Cook
Date :  22 Mar 16  (Deposition) - 15 Jun 16  (Release) - 15 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Translational Gtpase Ribosome Synthesis, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. M. Mccaughan, U. Jayachandran, V. Shchepachev, Z. A. Chen, J. Rappsilber, D. Tollervey, A. G. Cook
Pre-40S Ribosome Biogenesis Factor Tsr1 Is An Inactive Structural Mimic Of Translational Gtpases.
Nat Commun V. 7 11789 2016
PubMed-ID: 27250689  |  Reference-DOI: 10.1038/NCOMMS11789

(-) Compounds

Molecule 1 - RIBOSOME BIOGENESIS PROTEIN TSR1,RIBOSOME BIOGENESIS PROTEIN TSR1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: TSR1, YDL060W
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE, SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / S288C)
    Organism Taxid: 559292
    Synonym: 20S RRNA ACCUMULATION PROTEIN 1,20S RRNA ACCUMULATION PROTEIN 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5IW7)

(-) Sites  (0, 0)

(no "Site" information available for 5IW7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5IW7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5IW7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5IW7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5IW7)

(-) Exons   (0, 0)

(no "Exon" information available for 5IW7)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:595
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh........eeeeeee.....hhhhhhhhhhh...hhhhh......eeeeee....eeeeee.....hhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhh...eeeee.hhhhh..hhhhhhhhhhhhhhhhhhhh......ee..hhhhhhhhhhhhhhh....hhhhhh.eeee..eeeeee....eeeeeeeeeeee........eee...eee.eeeeeee....eee..............hhhh.ee...........ee.......hhh.ee......hhhhhh....ee...................hhhhh.ee.hhhhhhhhhhhhhhhh.......eeeeeeeee.hhhhhh........eeee.......eeeeeeeeee.............eeeee..eeeee..eeee.......eeeee........eeeeeeee......eeeeeee.......eeeeeeeeeee.....eeeeeeeeee.eeee....eee.....hhhhhhhh....eee....eeeeeee......eeeee........eeeeeeeee.....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iw7 A  67 LDSIENRKLFEGKNGAAKIITIVPLVNDLDPLDILYKLLKCADDEGIMVQESKRIFNVHIKKFKSNLKIIIPDMTNFLNILDCAKVADFVVFGLSGVQEVDEEFGEQIIRALELQGIASYIGVISNLSAVHEKEKFQLDVKQSLESYFKHFFPSEERVYNLEKNSDALNVLRTLCQRLPRSINWRDNRGYVVADFVDFVETSPDSGDLVIEGTVRGIGFNANRLVHIPDFGDFQLNKIEKISESTVFESNMNRDTLDEYAPEGTEDWSDYDEDFELTTARYDDHGFLDREFPDEIELEPSESAIERLKRYRGLKNLYNCDWQVDEKDPSSPAEWKRLLRIGNYKNTKNRIIKETKNEAQAIAGDRIRMFIRFPKFLLEKIQDPKQLLFAVYGLLLHEHKNAVVNFSLQRWEQYDKPVPSQEPIVVQYGVRRYTIQPLFSQGSNSPNNVHKYERFLHPDTVSVATCIAPVDFTQSPAIFFKPSPTDAKNIELIGHGTFLNADHSRILAKRAILTGHPFRFHKTVVTVRYMFFRPEDVEWFKSIPLFTKSGRSGFIKESLGTHGYFKATFDGLSAQDVVAMSLYKRMWPMPSLPWNG 787
                                    76        86        96       106       116||     128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308   ||  340       350       360    || 373      |481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761|      772       782     
                                                                            117|                                                                                                                                                                                             312|                           365|        380|                                                                                                                                                                                                                                                                                       761|                        
                                                                             120                                                                                                                                                                                              335                            369         479                                                                                                                                                                                                                                                                                        763                        


Chain B from PDB  Type:PROTEIN  Length:569
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.......eeeeeee.....hhhhhhhhhhh.........eeeeee....eeeeee.....hhhhhhhhhhhh.eeeeee.........hhhhhhhhhhhhh...eeeee.hhhhh.hhhhhhhhhhhhhhhhh......ee..hhhhhhhhhhhhhhh....hhhhhh.eeee..eeeeee....eeeeeeeee...........eee...eee.eeeeeee.eee..............hhhh.ee..................ee......hhhhhh.........................hhhhh.ee.hhhhhhhhhhhhhhhh.......eeeeeeeee.hhhhhh........eeee.......eeeeeeeeee.............eeeee..eeeee..eeee.......eeeee........eeeeeeee......eeeeeee.......eeeeeeeeeeee....eeeee.eeee..ee.....ee......hhhhhhhh....eee....eeeeee.......eeeee....eee..eeee.....ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iw7 B  70 IENRKLFEGKNGAAKIITIVPLVNDLDPLDILYKLLKCADDEGIMRIFNVHIKKFKSNLKIIIPDMTNFLNILDCAKVADFVVFGLSGVQEVDEEFGEQIIRALELQGIASYIGVISNLSAVKFQLDVKQSLESYFKHFFPSEERVYNLEKNSDALNVLRTLCQRLPRSINWRDNRGYVVADFVDFVETSPDSGDLVIEGTVRGIGFNANRLVHIPDFGDFQLNKIEKITVFESNMNRDTLDEYAPEGTEDWSDYDEDFEYDGTARYDDHPDEIELEPSESAIERLKRYRGLKNLYNCDWQVDEKDPSSPAEWKRLLRIGNYKNTKNRIIKETKNEAQAIAGDRIRMFIRFPKFLLEKIQDPKQLLFAVYGLLLHEHKNAVVNFSLQRWEQYDKPVPSQEPIVVQYGVRRYTIQPLFSQGSNSPNNVHKYERFLHPDTVSVATCIAPVDFTQSPAIFFKPSPTDAKNIELIGHGTFLNADHSRILAKRAILTGHPFRFHKTVVTVRYMFFRPEDVEWFKSIPLFTKSGRSGFIKESLGTHGYFKATFDGDVVAMSLYKRMWPMPSLPWN 786
                                    79        89        99       109    || 126       136       146       156       166       176       186       196 ||    210       220       230       240       250       260       270       280       290       300       335       345       355       365  ||   377|      492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       767       777         
                                                                      114|                                                                         198|                                                                                                       309|                              368|   377|                                                                                                                                                                                                                                                                                   761|                   
                                                                       122                                                                          203                                                                                                        335                               371    483                                                                                                                                                                                                                                                                                    767                   


Chain C from PDB  Type:PROTEIN  Length:567
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..eeeeeee.....hhhhhhhhhhh.......eeeee....eeeee.....hhhhhhhhhhhh.eeeeee.....hhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.....hhhhhh..eee..eeeeeeee..eeeeeeeee...........eee...eee.eeeeeee.....eee..............hhhh.ee.....hhhhh....ee......hhh.ee......hhhhhh....ee...................hhhhh.ee.hhhhhhhhhhhhhhhh.......eeeeeeeehhhhhhhh........eeee.......eeeeeeeeee.............eeeee..eeeee..eee........eeeee........eeeeeeee......eeeeeee....eeeeeeeee.......eeeeeeeeeeeeeeee..eeeee....hhhhhhhh....eee....eeeeeee.....eeeeee.........eeeeeeeee.....ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iw7 C  71 ENRKLFEGKNGAAKIITIVPLVNDLDPLDILYKLLKCADDSKRIFNVHIFKSNLKIIIPDMTNFLNILDCAKVADFVVFGLSGDEEFGEQIIRALELQGIASYIGVISNLSALDVKQSLESYFKHFFPSEYNLEKNSDALNVLRTLCQRLPRSINWRDNRGYVVADFVDFVETSPDSGDLVIEGTVRGIGFNANRLVHIPDFGDFQLNKIEKISELQTVFESNMNRDTLDEYAPEGTEDWSDYDEDFEYDGLTTARYDDHGFLREFPDEIELEPSESAIERLKRYRGLKNLYNCDWQVDEKDPSSPAEWKRLLRIGNYKNTKNRIIKETKNEAQAIAGDRIRMFIRFPKFLLEKIQDPKQLLFAVYGLLLHEHKNAVVNFSLQRWEQYDKPVPSQEPIVVQYGVRRYTIQPLFSQGSNSPNNVHKYERFLHPDTVSVATCIAPVDFTQSPAIFFKPSPKNIELIGHGTFLNADHSRILAKRAILTGHPFRFHKTVVTVRYMFFRPEDVEWFKSIPLFTKSGRSGFIKESLGTHGYFKATFDGKLSAQDVVAMSLYKRMWPMPSLPWN 786
                                    80        90       100       110|      131       141       151       161  ||   175       185       195 ||    213       223|      236       246       256       266       276       286       296       306    || 337       347       357       367       377  ||   486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       679       689       699       709       719       729       739       749       759       769       779       
                                                                 110|     128|                              164|                         197|              223|                                                                                 311|                                            380|                                                                                                                                                                                               674|                                                                                                            
                                                                  120      131                               169                          206               227                                                                                  333                                             480                                                                                                                                                                                                678                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:517
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.....hhhhhhhhhhh...eeeeee..eeeeee.....hhhhhhhhhhh..eeeee....hhhhhhhhhhhhh...eee........hhhhhhhhhhhhhhhh......hhhhhhhhhhhh....hhhhhhhheee..eeeee.......eeeeeee...........eee...eee.eeeee.ee..............hhhh.ee.........ee.........ee......hhhhhh....ee...................hhhhh.ee.hhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhh........eeee.......eeeeeeeeee.............eeeee..eeeee..eee........eeeee........eeeeeeee......eeeee...eeeeeee.....eeeeeeeeee....ee.....hhhhhhhh....eee....ee.eeee......eee......eeeeeeeee.....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iw7 D  81 GAAKIITIVPLVNDLDPLDILYKLLKCARIFNVHIKKSNLKIIIPDMTNFLNILDCAKVADFVVFGVDEEFGEQIIRALELQGIASYIGVISNLSAFQLDVKQSLESYFKHFFPSEERSDALNVLRTLCQRLPRSINWRDNRGYVVADFVDFVETSPDSGDLVIEGTVRGIGFNANRLVHIPDFGDFQLNKIEVFESNMNRDTLDEYAPEGTEDWSDYDEDFTTARYDDHGFLPGPDEIELEPSESAIERLKRYRGLKNLYNCDWQVDEKDPSSPAEWKRLLRIGNYKNTKNRIIKETKNEAQAIAGDRIRMFIRFPKFLLEKIQDPKQLLFAVYGLLLHEHKNAVVNFSLQRWEQYDKPVPSQEPIVVQYGVRRYTIQPLFSQGSNSPNNVHKYERFLHPDTVSVATCIAPVDFTQSPAIFFKLIGHGTFLNADHSRILAKRAILTGHPVVTVRYMFFRPEDVEWFKSIPLFTKSGRSGFIKESLGTHGYFKATSAQDVVAMSLYKRMWPMPSLPW 785
                                    90       100       123     ||135       145       155     ||171       181       191     ||207       217       234       244       254       264       274       284       294       304  ||   342       352       362 ||    377    || 487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667   ||  687       697       707|      723       733       743       753    || 768       778       
                                                     108|    129|                          161|                          197|                  225|                                                                       307|                         364|         382|                                                                                                                                                                                         671|                      707|                                         758|                     
                                                      122     132                           168                           204                   233                                                                        336                          370          483                                                                                                                                                                                          682                       714                                          764
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

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(no "SCOP Domain" information available for 5IW7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5IW7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5IW7)

(-) Gene Ontology  (11, 11)

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  TSR1_YEAST | Q07381
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        TSR1_YEAST | Q07381: 5wwn

(-) Related Entries Specified in the PDB File

1922 THIS EM VOLUME IS A NEGATIVE-STAIN SINGLE PARTICLE VOLUME REPORTED IN STRUNK ET AL 2011 OF YEAST TSR1. THIS VOLUME WAS USED FOR CROSS COMPARISON WITH OUR CRYSTAL STRUCTURE.
1926 THIS EM MAP IS A CRYOEM SINGLE PARTICLE RECONSTRUCTION OF WILD TYPE YEAST PRE40S PARTICLES, AS REPORTED IN STRUNK ET AL 2011. WE USED THIS VOLUME IN CONJUCTION WITH EMD1927 TO LOCATE TSR1 IN THE PRE- 40S PARTICLE.
1927 THIS EM MAP IS A CRYOEM SINGLE PARTICLE RECONSTRUCTION OF TSR1- DEPLETED YEAST PRE40S PARTICLES, AS REPORTED IN STRUNK ET AL 2011. WE USED THIS VOLUME IN CONJUCTION WITH EMD1926 TO LOCATE TSR1 IN THE PRE-40S PARTICLE.