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Crystal structure of CRM1 inhibitor Leptomycin B in complex with CRM1(K548E,K579Q)-Ran-RanBP1
Biology and Chemistry Report
4HAY
  •   Structure Details   Hide

    Structure Keywords

    Keywords PROTEIN TRANSPORT/ANTIBIOTIC
    Text HEAT repeat, nuclear export, Ran-RanBP1, LMB, leptomycin B, PROTEIN TRANSPORT-ANTIBIOTIC complex

    Polymeric Molecules

    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 
    Chain C
    Description Exportin-1 
    Fragment SEE REMARK 999 
    Mutation T539C,K548E,K579Q,Y1022C 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 117399.0 
    Source Method genetically manipulated  
    Entity Name CRM1, Chromosome region maintenance protein 1, Karyopherin-124 

    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 
    LMB  Leptomycin B, bound form  C33 H52 O7   560.76  View 
    MG  MAGNESIUM ION  Mg   24.31  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
    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. 
    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. 
    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. 
    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. 
    51301   Cell Division  The Process Resulting in the Physical Partitioning and Separation of a Cell Into Daughter Cells. 
    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. 
    42470   Melanosome  A Tissue Specific Membrane Bounded Cytoplasmic Organelle Within Which Melanin Pigments Are Synthesized and Stored. Melanosomes Are Synthesized in Melanocyte Cells. 
    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. 
    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. 
    Chain C
    GO ID   Ontology GO Term Definition
    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. 
    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. 
    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. 
    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). 


     
  •   Gene Details   Hide

    Genetic Source

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


    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  


    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     Crm1p 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 Coil 15% (Intermediate) 12 131357396 GNP
    rs11546492 LS-SNP   dbSNP   A 32 T - > I Helix 26% (Intermediate) 12 131357439
    rs199644788 LS-SNP   dbSNP   A 40 V - > FL Coil 77% (Exposed) 12 131357552 GNP,MG
    rs145207608 LS-SNP   dbSNP   A 55 N - > *Q Turn 54% (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 38% (Exposed) 12 131357640
    rs11546488 LS-SNP   dbSNP   A 95 R - > I Helix 60% (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 29% (Intermediate) 12 131360236
    rs1804272 LS-SNP   dbSNP   A 185 P - > L Coil 41% (Exposed) 12 131360275