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(-) Description

Title :  CRYSTAL STRUCTURE OF TANDEM ZPR1 DOMAINS
 
Authors :  A. K. Mishra
Date :  10 Jul 07  (Deposition) - 07 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Helical Hairpins, Beta Helix, Anti-Parrallel Beta Sheet, Double Straded Anti-Parallel Beta Helix, Metal Binding Protein, Signaling Protein, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Mishra, L. Gangwani, R. J. Davis, D. G. Lambright
Structural Insights Into The Interaction Of The Evolutionarily Conserved Zpr1 Domain Tandem With Eukaryotic Ef1A, Receptors, And Smn Complexes.
Proc. Natl. Acad. Sci. Usa V. 104 13930 2007
PubMed-ID: 17704259  |  Reference-DOI: 10.1073/PNAS.0704915104
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ZINC FINGER PROTEIN ZPR1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET15B MODIFIED
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneZNF259, ZFP259, ZPR1
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymZINC FINGER PROTEIN 259

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FMT1Ligand/IonFORMIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1FMT2Ligand/IonFORMIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:51 , CYS A:54 , CYS A:80 , CYS A:83BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWARECYS A:259 , CYS A:262 , CYS A:288 , CYS A:291BINDING SITE FOR RESIDUE ZN A 502
3AC3SOFTWAREARG A:56 , ARG A:310 , GLU A:334 , ILE A:404 , ASN A:406BINDING SITE FOR RESIDUE FMT A 778

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:419 -Pro A:420

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QKD)

(-) Exons   (0, 0)

(no "Exon" information available for 2QKD)

(-) 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:384
 aligned with ZPR1_MOUSE | Q62384 from UniProtKB/Swiss-Prot  Length:459

    Alignment length:394
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436    
           ZPR1_MOUSE    47 IESLCMNCYRNGTTRLLLTKIPFFREIIVSSFSCEHCGWNNTEIQSAGRIQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEGLISRAISGLEQDQPTRRAVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGLQAEAPEEKAEEEDLRNEVLQFNTNCPECNAPAQTNMKLVQIPHFKEVIIMATNCENCGHRTNEVKSGGAVEPLGTRITLHITDPSDMTRDLLKSETCSVEIPELEFELGMAVLGGKFTTLEGLLKDIRELVTKNPFTLGDSSNPDQSEKLQEFSQKLGQIIEGKMKAHFIMNDPAGNSYLQNVYAPEDDPEMKVERYKRTFDQNEE 440
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------zf-ZPR1-2qkdA01 A:256-416                                                                                                                                        ------------------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------zf-ZPR1-2qkdA02 A:256-416                                                                                                                                        ------------------------ Pfam domains (2)
         Sec.struct. author .eee......eeeeeeeeeee...eeeeeeeee......eeeeeeeee.....eeeeeeee.hhhhhh.eeee....eeeehhhheee.......eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.....ee...........eeeeee..hhhhhhhh..----------.......eeeeee..........eeeeee.......eeeeeee......eeeeeee.......eeeeeeee.hhhhhh.eeee....eeeehhhheee.......eeeehhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh....eeeeeee.....ee...........eeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qkd A  47 IESLCMNCYRNGTTRLLLTKIPFFREIIVSSFSCEHCGWNNTEIQSAGRIQDQGVRYTLTVRSQEDMNREVVKTDSATTRIPELDFEIPAFSQKGALTTVEGLISRAISGLEQDQPTRRAVEGAIAERIDEFIGKLKDLKQMASPFTLVIDDPSGNSFVENPHAPQKDNALVITYYDRTPQQAEMLGL----------EEDLRNEVLQFNTNCPECNAPAQTNMKLVQIPHFKEVIIMATNCENCGHRTNEVKSGGAVEPLGTRITLHITDPSDMTRDLLKSETCSVEIPELEFELGMAVLGGKFTTLEGLLKDIRELVTKNPFTLGDSSNPDQSEKLQEFSQKLGQIIEGKMKAHFIMNDPAGNSYLQNVYAPEDDPEMKVERYKRTFDQNEE 440
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       | -       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436    
                                                                                                                                                                                                                     234        245                                                                                                                                                                                                   

   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 2QKD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (39, 39)

Asymmetric Unit(hide GO term definitions)
Chain A   (ZPR1_MOUSE | Q62384)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0030971    receptor tyrosine kinase binding    Interacting selectively and non-covalently with a receptor that possesses protein tyrosine kinase activity.
    GO:0031369    translation initiation factor binding    Interacting selectively and non-covalently with a translation initiation factor, any polypeptide factor involved in the initiation of ribosome-mediated translation.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030576    Cajal body organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of Cajal bodies, nuclear bodies that appear ultrastructurally as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter and are enriched in ribonucleoproteins, and certain general RNA polymerase II transcription factors.
    GO:0042023    DNA endoreduplication    Regulated re-replication of DNA within a single cell cycle, resulting in an increased cell ploidy. An example of this process occurs in the synthesis of Drosophila salivary gland cell polytene chromosomes.
    GO:0008380    RNA splicing    The process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
    GO:1902742    apoptotic process involved in development    Any apoptotic process that is involved in anatomical structure development.
    GO:0061564    axon development    The progression of an axon over time. Covers axonogenesis (de novo generation of an axon) and axon regeneration (regrowth), as well as processes pertaining to the progression of the axon over time (fasciculation and defasciculation).
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0071364    cellular response to epidermal growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an epidermal growth factor stimulus.
    GO:0001833    inner cell mass cell proliferation    The proliferation of cells in the inner cell mass.
    GO:0006397    mRNA processing    Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
    GO:0000226    microtubule cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    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:2000672    negative regulation of motor neuron apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of motor neuron apoptotic process.
    GO:0033120    positive regulation of RNA splicing    Any process that activates or increases the frequency, rate or extent of RNA splicing.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0045927    positive regulation of growth    Any process that activates or increases the rate or extent of growth, the increase in size or mass of all or part of an organism.
    GO:0042307    positive regulation of protein import into nucleus    Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus.
    GO:0071931    positive regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that activates or increases transcription as part of the G1/S transition of the mitotic cell cycle.
    GO:1990261    pre-mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of the unspliced pre-mRNA (pre-messenger RNA).
    GO:0031641    regulation of myelination    Any process that modulates the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
    GO:0021510    spinal cord development    The process whose specific outcome is the progression of the spinal cord over time, from its formation to the mature structure. The spinal cord primarily conducts sensory and motor nerve impulses between the brain and the peripheral nervous tissues.
    GO:0001834    trophectodermal cell proliferation    The proliferation of cells in the trophectoderm.
cellular component
    GO:0015030    Cajal body    A class of nuclear body, first seen after silver staining by Ramon y Cajal in 1903, enriched in small nuclear ribonucleoproteins, and certain general RNA polymerase II transcription factors; ultrastructurally, they appear as a tangle of coiled, electron-dense threads roughly 0.5 micrometers in diameter; involved in aspects of snRNP biogenesis; the protein coilin serves as a marker for Cajal bodies. Some argue that Cajal bodies are the sites for preassembly of transcriptosomes, unitary particles involved in transcription and processing of RNA.
    GO:0097504    Gemini of coiled bodies    Nuclear bodies frequently found near or associated with Cajal bodies (also called coiled bodies or CBs). Gemini of coiled bodies, or 'gems', are similar in size and shape to CBs, and often indistinguishable under the microscope. Unlike CBs, gems do not contain small nuclear ribonucleoproteins (snRNPs); they contain a protein called survivor of motor neurons (SMN) whose function relates to snRNP biogenesis. Gems are believed to assist CBs in snRNP biogenesis, and to play a role in the etiology of spinal muscular atrophy (SMA).
    GO:0032797    SMN complex    A protein complex that contains the survival motor neuron (SMN) protein and at least eight additional integral components, including the Gemin2-8 and Unrip proteins; the complex is found in the cytoplasm and in nuclear Gems, and is involved in spliceosomal snRNP assembly in the cytoplasm and in pre-mRNA splicing in the nucleus.
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0042995    cell projection    A prolongation or process extending from a cell, e.g. a flagellum or axon.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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: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.
    GO:0043204    perikaryon    The portion of the cell soma (neuronal cell body) that excludes the nucleus.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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