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(-) Description

Title :  THE SOLUTION STRUCTURE OF HOMEODOMAIN-PROTEIN COMPLEX
 
Authors :  C. Liu, B. Zhou, Z. Xu, G. Zhu
Date :  29 Jan 12  (Deposition) - 06 Jun 12  (Release) - 06 Jun 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (10x)
NMR Structure *:  A,B  (1x)
Keywords :  Homeodomain, Transcription-Cell Cycle Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Zhou, C. Liu, Z. Xu, G. Zhu
Structural Basis For Homeodomain Recognition By The Cell-Cycle Regulator Geminin
Proc. Natl. Acad. Sci. Usa 2012
PubMed-ID: 22615398  |  Reference-DOI: 10.1073/PNAS.1200874109

(-) Compounds

Molecule 1 - HOMEOBOX PROTEIN HOX-C9
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET32
    Expression System Vector TypeVECTOR
    FragmentUNP RESIDUES 192-251
    GeneHOXC9
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHOMEOBOX PROTEIN HOX-3B
 
Molecule 2 - GEMININ
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET32
    Expression System Vector TypeVECTOR
    FragmentUNP RESIDUES 171-190
    GeneGMNN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x)AB
NMR Structure * (1x)AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2LP0)

(-) Sites  (0, 0)

(no "Site" information available for 2LP0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LP0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LP0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2LP0)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.HXC9_HUMAN225-248  1A:50-73
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.HXC9_HUMAN225-248  1A:50-73

(-) Exons   (1, 1)

NMR Structure (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003565091aENSE00001917299chr6:24775159-24775340182GEMI_HUMAN-00--
1.3bENST000003565093bENSE00000848247chr6:24777450-2477752576GEMI_HUMAN1-17170--
1.4ENST000003565094ENSE00000693554chr6:24780891-2478096878GEMI_HUMAN18-43260--
1.5bENST000003565095bENSE00000693556chr6:24781705-24781849145GEMI_HUMAN44-92490--
1.6bENST000003565096bENSE00000693558chr6:24784315-2478439783GEMI_HUMAN92-119280--
1.7ENST000003565097ENSE00000693560chr6:24784672-24784782111GEMI_HUMAN120-156370--
1.8bENST000003565098bENSE00001419614chr6:24785866-24786323458GEMI_HUMAN157-209531B:171-19020

(-) Sequences/Alignments

NMR Structure
   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:60
 aligned with HXC9_HUMAN | P31274 from UniProtKB/Swiss-Prot  Length:260

    Alignment length:60
                                   201       211       221       231       241       251
           HXC9_HUMAN   192 TRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN 251
               SCOP domains d2lp0a_ A: automated matches                                 SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------HOMEOBOX_1  PDB: A:50-73--- PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                 2lp0 A  17 TRKKRCPYTKYQTLELEKEFLFNMYLTRDRRYEVARVLNLTERQVKIWFQNRRMKMKKMN  76
                                    26        36        46        56        66        76

Chain B from PDB  Type:PROTEIN  Length:20
 aligned with GEMI_HUMAN | O75496 from UniProtKB/Swiss-Prot  Length:209

    Alignment length:20
                                   180       190
           GEMI_HUMAN   171 NQEFDSEEETVEDSLVEDSE 190
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .................... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
               Transcript 1 Exon 1.8b            Transcript 1
                 2lp0 B 171 NQEFDSEEETVEDSLVEDSE 190
                                   180       190

   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  (1, 1)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LP0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LP0)

(-) Gene Ontology  (23, 25)

NMR Structure(hide GO term definitions)
Chain A   (HXC9_HUMAN | P31274)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
biological process
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0048706    embryonic skeletal system development    The process, occurring during the embryonic phase, whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure.
    GO:0048704    embryonic skeletal system morphogenesis    The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    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.

Chain B   (GEMI_HUMAN | O75496)
molecular function
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
biological process
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0008156    negative regulation of DNA replication    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA replication.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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

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

UniProtKB/Swiss-Prot
        GEMI_HUMAN | O754961t6f 1uii 2wvr 4bry
        HXC9_HUMAN | P312742msy

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