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(-) Description

Title :  STRUCTURE OF THE CTD COMPLEX OF UTP12, UTP13, UTP1 AND UTP21
 
Authors :  C. Zhang, K. Ye
Date :  23 Feb 16  (Deposition) - 06 Jul 16  (Release) - 14 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.51
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Rrna Processing, 90S Preribosome, Protein Binding, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Zhang, Q. Sun, R. Chen, X. Chen, J. Lin, K. Ye
Integrative Structural Analysis Of The Utpb Complex, An Early Assembly Factor For Eukaryotic Small Ribosomal Subunits
Nucleic Acids Res. V. 44 7475 2016
PubMed-ID: 27330138  |  Reference-DOI: 10.1093/NAR/GKW562

(-) Compounds

Molecule 1 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 769-931
    Gene: CTHT_0003430
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
    Synonym: U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 12
 
Molecule 2 - PUTATIVE UNCHARACTERIZED PROTEIN
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 738-889
    Gene: CTHT_0065530
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
    Synonym: U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 13
 
Molecule 3 - PUTATIVE U3 SNORNP PROTEIN
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 806-1049
    Gene: CTHT_0037800
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
    Synonym: U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 21
 
Molecule 4 - PERIODIC TRYPTOPHAN PROTEIN 2-LIKE PROTEIN
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 701-849
    Gene: CTHT_0061240
    Organism Scientific: CHAETOMIUM THERMOPHILUM (STRAIN DSM 1495 / CBS 144.50 / IMI 039719)
    Organism Taxid: 759272
    Strain: DSM 1495 / CBS 144.50 / IMI 039719
    Synonym: U3 SMALL NUCLEOLAR RNA-ASSOCIATED PROTEIN 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5ICA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp B:784 -Pro B:785

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ICA)

(-) 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:163
                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ica A  769 TKQTVETLMAGERIAEALELGMTDLNTIREWEEARQINPNIAPPQRNPIFVALGNIPAETYVLNTLQKIKPASLHDALLVLPFSTIPSLLTFLNLFAQRELNVPLTCRILFFVLKTHHKQIVASRTMRATLEKVRANLRAALRRQKDEMGFNIAALKVVSMQL  931
                                   778       788       798       808       818       828       838       848       858       868       878       888       898       908       918       928   


Chain B from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhh...........hhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5ica B  744 TLENYIHAGAYRDAIVLALQLNHPGRLLNLFTNVVTTRNPDPDSLTGLKAVDDVLAKLSDEQIFQLLLRLRDWNTNARTAPVAQRVLWALFKSHPANKLSSLSSLNEVLDAIKVYTERHYKRIEELVDESYLVEYTLR  889
                                   753       763       773       783       793       803       813       823       833       843  ||   861       871       881        
                                                                                                                                846|                                  
                                                                                                                                 855                                  


Chain C from PDB  Type:PROTEIN  Length:128
                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhh.hhhhhhh.....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ica C  900 KKEKAAANGASRTFTSKLLVGGAKGDYTDFIEHLKALPPAAADLELDEATNELLHFIRALTSRLVARRDYELTQAWMTVFLRLHFDLIMENEELLQALGEWREHQARERDRLSELVGYCGGVVSFLRS 1046
                                   909 ||    930       940       950     ||968       978       988       998      1008      1018      1028      1038        
                                     911|                              956|                                                                                 
                                      923                               965                                                                                 


Chain D from PDB  Type:PROTEIN  Length:119
                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.hhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                5ica D  729 DYLKALVMAFRLNEAGLITRVYQAIPYTDIGLVVEQFPTVYVPRLLRFVAAQTEQSPHMEFCLLWIRALIDKHGPWLAANRGKVDVELRVVARAVAKMRDEIRRLADENVYMVDYLLNQ  847
                                   738       748       758       768       778       788       798       808       818       828       838
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  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 5ICA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 5ica)
 
  Cis Peptide Bonds
    Asp B:784 - Pro B:785   [ RasMol ]  
 

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 Related Entries

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

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        G0RZL9_CHATD | G0RZL9: 5ic9
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(-) Related Entries Specified in the PDB File

5ic7 5ic8 5ic9