POP-OUT | CLOSE

An Information Portal to 105339 Biological Macromolecular Structures

Crystal structure of CRM1 inhibitor Ratjadone A in complex with CRM1(K579A)-Ran-RanBP1
Biology and Chemistry Report
4HAX
  •   Structure Details   Hide

    Structure Keywords

    Keywords PROTEIN TRANSPORT/ANTIBIOTIC
    Text HEAT repeat, nuclear export, Ran-RanBP1, Ratjadone A, PROTEIN TRANSPORT-ANTIBIOTIC complex

    Polymeric Molecules

    Chain C
    Description Exportin-1 
    Fragment SEE REMARK 999 
    Mutation T539C,K579A,Y1022C 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 117342.0 
    Source Method genetically manipulated  
    Entity Name CRM1, Chromosome region maintenance protein 1, Karyopherin-124 
    Chain A
    Description GTP-binding nuclear protein Ran 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 24456.3 
    Source Method genetically manipulated  
    Entity Name Androgen receptor-associated protein 24, GTPase Ran, Ras-like protein TC4, Ras-related nuclear protein 
    Chain B
    Description Ran-specific GTPase-activating protein 1 
    Fragment RanDB1 (UNP residues 62-201) 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 16378.9 
    Source Method genetically manipulated  
    Entity Name Chromosome stability protein 20, Perinuclear array-localized protein, Ran-binding protein 1, RANBP1 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    CL  CHLORIDE ION  Cl   35.45  View 
    EDO  1,2-ETHANEDIOL  C2 H6 O2   62.07  View 
    GNP  PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER  C10 H17 N6 O13 P3   522.20  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    RJA  Ratjadone A, bound form  C28 H44 O6   476.65  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A RAN_HUMAN A8K3Z8     
    B YRB1_YEAST D6VRY9     
    C XPO1_YEAST D6VV01     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A
    GO ID   Ontology GO Term Definition
    55   Ribosomal Large Subunit Export From Nucleus  The Directed Movement of a Ribosomal Large Subunit From the Nucleus Into the Cytoplasm. 
    56   Ribosomal Small Subunit Export From Nucleus  The Directed Movement of a Ribosomal Small Subunit From the Nucleus Into the Cytoplasm. 
    6184   GTP Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of GTP Guanosine Triphosphate. 
    6259   DNA Metabolic Process  Any Cellular Metabolic Process Involving Deoxyribonucleic Acid. This Is One of the Two Main Types of Nucleic Acid Consisting of a Long Unbranched Macromolecule Formed From One or More Commonly Two Strands of Linked Deoxyribonucleotides. 
    6611   Protein Export From Nucleus  The Directed Movement of a Protein From the Nucleus Into the Cytoplasm. 
    6810   Transport  The Directed Movement of Substances (such As Macromolecules Small Molecules Ions) Into Out of or Within a Cell or Between Cells or Within a Multicellular Organism by Means of Some Agent Such As a Transporter or Pore. 
    6886   Intracellular Protein Transport  The Directed Movement of Proteins in a Cell Including the Movement of Proteins Between Specific Compartments or Structures Within a Cell Such As Organelles of a Eukaryotic Cell. 
    6913   Nucleocytoplasmic Transport  The Directed Movement of Molecules Between the Nucleus and the Cytoplasm. 
    7049   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. 
    7052   Mitotic Spindle Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of the Microtubule Spindle During a Mitotic Cell Cycle. 
    7067   Mitotic Nuclear Division  A Cell Cycle Process Comprising the Steps by Which the Nucleus of a Eukaryotic Cell Divides; the Process Involves Condensation of Chromosomal DNA Into a Highly Compacted Form. Canonically Mitosis Produces Two Daughter Nuclei Whose Chromosome Complement Is Identical to That of the Mother Cell. 
    7165   Signal Transduction  The Cellular Process in Which a Signal Is Conveyed to Trigger a Change in the Activity or State of a Cell. Signal Transduction Begins with Reception of a Signal (e.g. a Ligand Binding to a Receptor or Receptor Activation by a Stimulus Such As Light) or For Signal Transduction in the Absence of Ligand Signal Withdrawal or the Activity of a Constitutively Active Receptor. Signal Transduction Ends with Regulation of a Downstream Cellular Process E.g. Regulation of Transcription or Regulation of a Metabolic Process. Signal Transduction Covers Signaling From Receptors Located On the Surface of the Cell and Signaling Via Molecules Located Within the Cell. For Signaling Between Cells Signal Transduction Is Restricted to Events At and Within the Receiving Cell. 
    7264   Small Gtpase Mediated Signal Transduction  Any Series of Molecular Signals in Which a Small Monomeric Gtpase Relays One or More of the Signals. 
    7286   Spermatid Development  The Process Whose Specific Outcome Is the Progression of a Spermatid Over Time From Its Formation to the Mature Structure. 
    10467   Gene Expression  The Process in Which a Gene's 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 (for Protein Coding Genes) and the Translation of That MRNA Into Protein. Some Protein Processing Events May Be Included When They Are Required to Form an Active Form of a Product From an Inactive Precursor Form. 
    15031   Protein Transport  The Directed Movement of Proteins Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 
    16032   Viral Process  A Multi Organism Process in Which a Virus Is a Participant. the Other Participant Is the Host. Includes Infection of a Host Cell Replication of the Viral Genome and Assembly of Progeny Virus Particles. in Some Cases the Viral Genetic Material May Integrate Into the Host Genome and Only Subsequently Under Particular Circumstances 'complete' Its Life Cycle. 
    19058   Viral Life Cycle  A Set of Processes Which All Viruses Follow to Ensure Survival; Includes Attachment and Entry of the Virus Particle Decoding of Genome Information Translation of Viral MRNA by Host Ribosomes Genome Replication and Assembly and Release of Viral Particles Containing the Genome. 
    30521   Androgen Receptor Signaling Pathway  Any Series of Molecular Signals Generated As a Consequence of an Androgen Binding to Its Receptor. 
    32092   Positive Regulation of Protein Binding  Any Process That Activates or Increases the Frequency Rate or Extent of Protein Binding. 
    44281   Small Molecule Metabolic Process  The Chemical Reactions and Pathways Involving Small Molecules Any Low Molecular Weight Monomeric Non Encoded Molecule. 
    45893   Positive Regulation of Transcription DNA Templated  Any Process That Activates or Increases the Frequency Rate or Extent of Cellular DNA Templated Transcription. 
    51301   Cell Division  The Process Resulting in Division and Partitioning of Components of a Cell to Form More Cells; May or May Not Be Accompanied by the Physical Separation of a Cell Into Distinct Individually Membrane Bounded Daughter Cells. 
    75733   Intracellular Transport of Virus  The Directed Movement of a Virus or Part of a Virus Within the Host Cell. 
    785   Chromatin  The Ordered and Organized Complex of DNA Protein and Sometimes RNA That Forms the Chromosome. 
    5622   Intracellular  The Living Contents of a Cell; the Matter Contained Within (but Not Including) the Plasma Membrane Usually Taken to Exclude Large Vacuoles and Masses of Secretory or Ingested Material. in Eukaryotes It Includes the Nucleus and Cytoplasm. 
    5634   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. 
    5643   Nuclear Pore  Any of the Numerous Similar Discrete Openings in the Nuclear Envelope of a Eukaryotic Cell Where the Inner and Outer Nuclear Membranes Are Joined. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5829   Cytosol  The Part of the Cytoplasm That Does Not Contain Organelles But Which Does Contain Other Particulate Matter Such As Protein Complexes. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    42470   Melanosome  A Tissue Specific Membrane Bounded Cytoplasmic Organelle Within Which Melanin Pigments Are Synthesized and Stored. Melanosomes Are Synthesized in Melanocyte Cells. 
    43234   Protein Complex  Any Macromolecular Complex Composed (only) of Two or More Polypeptide Subunits Along with Any Covalently Attached Molecules (such As Lipid Anchors or Oligosaccharide) or Non Protein Prosthetic Groups (such As Nucleotides or Metal Ions). Prosthetic Group in This Context Refers to a Tightly Bound Cofactor. the Component Polypeptide Subunits May Be Identical. 
    55037   Recycling Endosome  Organelle Consisting of Networks of 60nm Tubules Organized Around the Microtubule Organizing Centre in Some Cell Types. They Transport Molecules (e.g. Receptors Transporters Lipids) Derived From Endosomes the Golgi Apparatus or the Cytoplasm to the Plasma Membrane. Transported Molecules May Be Recycled For Reuse or May Be Newly Synthesized. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    3682   Chromatin Binding  Interacting Selectively and Non Covalently with Chromatin the Network of Fibers of DNA Protein and Sometimes RNA That Make Up the Chromosomes of the Eukaryotic Nucleus During Interphase. 
    3713   Transcription Coactivator Activity  Interacting Selectively and Non Covalently with a Activating Transcription Factor and Also with the Basal Transcription Machinery in Order to Increase the Frequency Rate or Extent of Transcription. Cofactors Generally Do Not Bind the Template Nucleic Acid But Rather Mediate Protein Protein Interactions Between Activating Transcription Factors and the Basal Transcription Machinery. 
    3924   Gtpase Activity  Catalysis of the Reaction: GTP + H2o = GDP + Phosphate. 
    5515   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). 
    5525   GTP Binding  Interacting Selectively and Non Covalently with GTP Guanosine Triphosphate. 
    19003   GDP Binding  Interacting Selectively and Non Covalently with GDP Guanosine 5' Diphosphate. 
    19904   Protein Domain Specific Binding  Interacting Selectively and Non Covalently with a Specific Domain of a Protein. 
    44822   Poly(a) RNA Binding  Interacting Non Covalently with a Poly(a) RNA a RNA Molecule Which Has a Tail of Adenine Bases. 
    50681   Androgen Receptor Binding  Interacting Selectively and Non Covalently with an Androgen Receptor. 
    Chain B
    GO ID   Ontology GO Term Definition
    46907   Intracellular Transport  The Directed Movement of Substances Within a Cell. 
    Chain C
    GO ID   Ontology GO Term Definition
    55   Ribosomal Large Subunit Export From Nucleus  The Directed Movement of a Ribosomal Large Subunit From the Nucleus Into the Cytoplasm. 
    6406   MRNA Export From Nucleus  The Directed Movement of MRNA From the Nucleus to the Cytoplasm. 
    6611   Protein Export From Nucleus  The Directed Movement of a Protein From the Nucleus Into the Cytoplasm. 
    6810   Transport  The Directed Movement of Substances (such As Macromolecules Small Molecules Ions) Into Out of or Within a Cell or Between Cells or Within a Multicellular Organism by Means of Some Agent Such As a Transporter or Pore. 
    6886   Intracellular Protein Transport  The Directed Movement of Proteins in a Cell Including the Movement of Proteins Between Specific Compartments or Structures Within a Cell Such As Organelles of a Eukaryotic Cell. 
    15031   Protein Transport  The Directed Movement of Proteins Into Out of or Within a Cell or Between Cells by Means of Some Agent Such As a Transporter or Pore. 
    34501   Protein Localization to Kinetochore  Any Process in Which a Protein Is Transported to or Maintained At the Kinetochore. 
    776   Kinetochore  A Multisubunit Complex That Is Located At the Centromeric Region of DNA and Provides an Attachment Point For the Spindle Microtubules. 
    5634   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. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    5816   Spindle Pole Body  The Microtubule Organizing Center in Fungi; Functionally Homologous to the Animal Cell Centrosome. 
    48471   Perinuclear Region of Cytoplasm  Cytoplasm Situated Near or Occurring Around the Nucleus. 
    5515   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). 
    8536   Ran Gtpase Binding  Interacting Selectively and Non Covalently with Ran a Conserved Ras Like GTP Binding Protein Implicated in Nucleocytoplasmic Transport Cell Cycle Progression Spindle Assembly Nuclear Organization and Nuclear Envelope (ne) Assembly. 
    8565   Protein Transporter Activity  Enables the Directed Movement of Proteins Into Out of or Within a Cell or Between Cells. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain B
    Common Name Yeast
    Scientific Name Saccharomyces cerevisiae  
    Gene yrb1, cst20, htn1, sfo1, ydr002w, yd8119.08
    Host Scientific Name Escherichia coli  


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ran, ara24, ok/sw-cl.81
    Host Scientific Name Escherichia coli  


    Chain C
    Common Name Yeast
    Scientific Name Saccharomyces cerevisiae  
    Gene crm1, kap124, xpo1, ygr218w, g8514
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    12 12q24.3 5901     RAN, member RAS oncogene family RAN    
    IV - 851565     Yrb1p YRB1    
    VII - 853133     exportin CRM1 CRM1    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs200416921 LS-SNP   dbSNP   A 18 D - > Y Bend 13% (Intermediate) 12 131357396 GNP
    rs11546492 LS-SNP   dbSNP   A 32 T - > I Helix 20% (Intermediate) 12 131357439
    rs199644788 LS-SNP   dbSNP   A 40 V - > FL Coil 81% (Exposed) 12 131357552 GNP,MG
    rs145207608 LS-SNP   dbSNP   A 55 N - > *Q Turn 50% (Exposed) 12 131357591
    rs114011062 LS-SNP   dbSNP   A 56 R - > G Turn 58% (Exposed) 12 131357594
    rs11546494 LS-SNP   dbSNP   A 72 F - > L 3/10 Helix 34% (Intermediate) 12 131357640
    rs11546488 LS-SNP   dbSNP   A 95 R - > I Helix 65% (Exposed) 12 131359127
    rs200176335 LS-SNP   dbSNP   A 115 I - > V Coil 19% (Intermediate) 12 131359186
    rs11546495 LS-SNP   dbSNP   A 172 P - > H Turn 32% (Intermediate) 12 131360236
    rs1804272 LS-SNP   dbSNP   A 185 P - > L Coil 44% (Exposed) 12 131360275