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(-) Description

Title :  STRUCTURE OF YTM1 BOUND TO THE C-TERMINAL DOMAIN OF ERB1 IN P21 21 2 SPACE GROUP
 
Authors :  M. Wegrecki, J. Bravo
Date :  28 Jul 15  (Deposition) - 04 Nov 15  (Release) - 23 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribosome Assembly, Wd40, Beta-Propeller, Ubiquitin-Like Domain, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Wegrecki, O. Rodriguez-Galan, J. De La Cruz, J. Bravo
The Structure Of Erb1-Ytm1 Complex Reveals The Functional Importance Of A High-Affinity Binding Between Two Beta-Propellers During The Assembly Of Large Ribosomal Subunits In Eukaryotes.
Nucleic Acids Res. V. 43 11017 2015
PubMed-ID: 26476442  |  Reference-DOI: 10.1093/NAR/GKV1043

(-) Compounds

Molecule 1 - RIBOSOME BIOGENESIS PROTEIN YTM1
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: POPINF
    Expression System Taxid: 7108
    Expression System Vector Type: PLASMID
    Gene: YTM1, CTHT_0061460
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 209285
 
Molecule 2 - RIBOSOME BIOGENESIS PROTEIN ERB1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET28-NKI/LIC 6HIS/3C
    Expression System Taxid: 469008
    Expression System Variant: CODON PLUS
    Expression System Vector Type: PLASMID
    Gene: ERB1, CTHT_0057570
    Organism Scientific: CHAETOMIUM THERMOPHILUM
    Organism Taxid: 209285
    Synonym: EUKARYOTIC RIBOSOME BIOGENESIS PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL2Ligand/IonGLYCEROL
4NA1Ligand/IonSODIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:181 , ASP A:229 , HOH A:684 , HOH A:688binding site for residue EDO A 501
2AC2SOFTWAREASP A:64 , SER A:98 , LEU A:99 , ASP A:417 , ARG A:419binding site for residue EDO A 502
3AC3SOFTWAREILE A:41 , ARG A:42 , GLY A:45binding site for residue EDO A 503
4AC4SOFTWAREGLU A:442 , ARG A:443 , TRP A:446 , ARG A:454 , HOH A:829binding site for residue NA A 504
5AC5SOFTWARETHR A:58 , SER A:60 , ILE A:61 , LYS A:256 , ALA A:257 , ARG A:287binding site for residue GOL A 505
6AC6SOFTWAREGLN B:487binding site for residue CL B 901
7AC7SOFTWAREHIS B:597 , ARG B:598 , ARG B:599 , ARG B:645 , PRO B:646binding site for residue GOL B 902

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys B:439 -Pro B:440

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CXB)

(-) Sequences/Alignments

Asymmetric/Biological 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:465
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhh.hhhh.eeeee...hhhhhhhhhhh..........eeeee..ee...hhhhhhhhh......eeeeeeee.....eeeeeee....eeeeeee...hhhhhhhhh............eeeeee....eeeee....eeee..hhhhh.....eeeeeeee..eeeeee...eeeeeeeee.....eeeeeeeeee.....eeeeeee....eeeeee....eeeee.........hhhhh.......eee...eee......eeeeee......eeeeee...eeeeee.....eeeeee....eeeeeee........eeeeee....eeee..........eee......eeeeee......eeeeee....eeeee....ee.hhhhh...eee.eeeee.hhhhhh......hhhhh...eeeeeee..eeeeee...eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cxb A  12 VAQVKVIFTTTEPDLELPESKRQLLVPADIRRYGLSRILNSESMLDTGSIPFDFLINGSFLRSSLEDYLTSNGLSLETTLTLQYVRSLIPPVYEASFEHDDWVSAVDVLSATSPAGRWSSAANSSAAVQPGQERVLSASYDGLLRIWNASGSVIATSPSGSHGGHTASIKAAKFLTSDRLASAGMDRTVRVWKYTESDHFTGELKPTLELYGHTGSVDWLDVDGHSKHILTASADGAIGFWSASKASAPEPDASLLPGAHVSTAQRGPLGLWSIHTAPATAAIFDPRDRTVAYSASQDHTVRTLDLTTGQVVSTLTLTHPLLSLSALTRAGTTSPLLAAGTSARHITMVDPRASSATTVMTLRGHANKVVSLSPSPENEYSLVSGSHDGTCRVWDLRSVRPATKEEGSLGGVSEPVYVIERESWASKGKKKRPVAGDGCKVFSVVWDKLGIFSGGEDKKVQVNRG 487
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271||     291       301       311       321       331       341       351       361       371       382       392       402       412       422       432       442       452       462       472       482     
                                                                                                                                                                                                                                                                                              272|                                                                                             379|                                                                                                          
                                                                                                                                                                                                                                                                                               283                                                                                              381                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....eeeeee......eeeeee.....eeeeee...eeeeee.....eeeeee......eeeeee........eeeee..eeeee.......hhhhhhhhhhhhhh.....eee..hhhhhhh.eeeeee......eeee.....eeeee.hhhh...eeeee....eee.........eeeeee.....eeeeee...eeeee.......eee......eeeeee.....eeeeee....eeeee........eee......eeeeee......eeeeee...eeeeeeee.........eeeeeeeee.........eeeeee......eeeee....eeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cxb B 433 PSPDELKPFPTVQQTIFRGHEGRVRSVAIDPTGVALATGGDDGTVRVWELLTGRQVWSVKLNGDEAVNTVRWRPTKDTFILAAAAGEDIFLMIPTHPSVTPALDQASRDILNAGFPPGKWARPGTRLEDEGVLLRITVRSTIKAISWHRRGDHFATVSPSGQRSSVAIHTLSKHLTQIPFRKLNGLAQTASFHPLRPLFFVATQRSIRCYDLQKLELVKIVQPGAKWISSFDVHPGGDNLVVGSYDKRLLWHDLDLSNRPYKTMRFHTEAIRAVRFHKGGLPLFADASDDGSLQIFHGKVPNDQLENPTIVPVKMLKGHKVVNKLGVLDIDWHPREPWCVSAGADGTARLWM 801
                                   442       452       462       472       482       492       502       512       522       532       542    || 569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799  
                                                                                                                                            547|                                                                                                                                                                                                                                            
                                                                                                                                             565
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 20)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys B:439 - Pro B:440   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ERB1_CHATD | G0SCK6: 5cxc 5cyk 5em2
        YTM1_CHATD | G0SFB5: 5cxc 5cyk 5em2

(-) Related Entries Specified in the PDB File

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