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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DUF55 DOMAIN OF HUMAN THYMOCYTE NUCLEAR PROTEIN 1
 
Authors :  F. Yu, A. Song, C. Xu, L. Sun, L. Li, L. Tang, H. Hu, J. He
Date :  29 Sep 08  (Deposition) - 29 Sep 09  (Release) - 17 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Unknown Function, Nucleus, Phosphoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Yu, A. Song, C. Xu, L. Sun, J. Li, L. Tang, M. Yu, T. O. Yeates, H. Hu, J. H
Determining The Duf55-Domain Structure Of Human Thymocyte Nuclear Protein 1 From Crystals Partially Twinned By Tetartohedry
Acta Crystallogr. , Sect. D V. 65 212 2009
PubMed-ID: 19237743  |  Reference-DOI: 10.1107/S0907444908041474

(-) Compounds

Molecule 1 - THYMOCYTE NUCLEAR PROTEIN 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22
    Expression System StrainROSETTA(DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentDUF55 DOMAIN, UNP RESIDUES 55-221
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTHYMOCYTE PROTEIN THY28

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:93 , ARG A:94 , SER A:204BINDING SITE FOR RESIDUE SO4 A 1
2AC2SOFTWAREARG A:200 , GLN A:201 , ARG A:202 , HIS B:56BINDING SITE FOR RESIDUE SO4 A 3
3AC3SOFTWAREVAL B:93 , ARG B:94 , ASN B:95 , ARG B:202 , SER B:204BINDING SITE FOR RESIDUE SO4 B 2
4AC4SOFTWAREHIS A:56 , THR B:199 , ARG B:200 , ARG B:202BINDING SITE FOR RESIDUE SO4 B 4

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:118 -B:118

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EOP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EOP)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EOP)

(-) Exons   (0, 0)

(no "Exon" information available for 3EOP)

(-) 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:169
 aligned with THYN1_HUMAN | Q9P016 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:169
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
          THYN1_HUMAN    55 SHWLMKSEPESRLEKGVDVKFSIEDLKAQPKQTTCWDGVRNYQARNFLRAMKLGEEAFFYHSNCKEPGIAGLMKIVKEAYPDHTQFEKNNPHYDPSSKEDNPKWSMVDVQFVRMMKRFIPLAELKSYHQAHKATGGPLKNMVLFTRQRLSIQPLTQEEFDFVLSLEEKE 223
               SCOP domains d3eopa_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...............hhhhhhhhh.eee.....hhhhhhhhhhh....eeeeee......eeeeeeeeeeeeee.hhhh..................eeeeeeeeeeeeeeeehhhhhhhhhhhhhhh.....hhhhhh....eeeehhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eop A  55 SHWLMKSEPESRLEKGVDVKFSIEDLKAQPKQTTCWDGVRNYQARNFLRAMKLGEEAFFYHSNCKEPGIAGLMKIVKEAYPDHTQFEKNNPHYDPSSKEDNPKWSMVDVQFVRMMKRFIPLAELKSYHQAHKATGGPLKNMVLFTRQRLSIQPLTQEEFDFVLSLEELE 223
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with THYN1_HUMAN | Q9P016 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:169
                                    64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
          THYN1_HUMAN    55 SHWLMKSEPESRLEKGVDVKFSIEDLKAQPKQTTCWDGVRNYQARNFLRAMKLGEEAFFYHSNCKEPGIAGLMKIVKEAYPDHTQFEKNNPHYDPSSKEDNPKWSMVDVQFVRMMKRFIPLAELKSYHQAHKATGGPLKNMVLFTRQRLSIQPLTQEEFDFVLSLEEKE 223
               SCOP domains d3eopb_ B        : automated matches                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...--------....hhhhhhhh...eee.....hhhhhhhhhhh....eeeeee......eeeeeeee....ee.hhhhh.................ee.eeeeeeeeeeeeehhhhhhhhhhhhhh......hhhhhh....eeeehhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eop B  55 SHWLMKSEP--------DVKFSIEDLKAQPKQTTCWDGVRNYQARNFLRAMKLGEEAFFYHSNCKEPGIAGLMKIVKEAYPDHTQFEKNNPHYDPSSKEDNPKWSMVDVQFVRMMKRFIPLAELKSYHQAHKATGGPLKNMVLFTRQRLSIQPLTQEEFDFVLSLEELE 223
                                    |-       |74        84        94       104       114       124       134       144       154       164       174       184       194       204       214         
                                   63       72                                                                                                                                                       

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EOP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EOP)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (THYN1_HUMAN | Q9P016)
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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        THYN1_HUMAN | Q9P0165j3e

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