POP-OUT | CLOSE
 
Crystal structure of the CBC-importin alpha complex.
Biology and Chemistry Report
3FEX
  •   Structure Details   Hide

    Structure Keywords

    Keywords TRANSLATION, PROTEIN TRANSPORT
    Text Cap binding complex, importin alpha, nuclear transport, mRNA transport, Nucleus, Phosphoprotein, RNA-binding, Host-virus interaction, TRANSLATION, PROTEIN TRANSPORT

    Polymeric Molecules

    Chain A
    Description Nuclear cap-binding protein subunit 1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 91961.1 
    Source Method genetically manipulated  
    Entity Name Cap binding protein 80; 80 kDa nuclear cap-binding protein; NCBP 80 kDa subunit; CBP80 
    Chain B
    Description Nuclear cap-binding protein subunit 2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 18028.3 
    Source Method genetically manipulated  
    Entity Name Cap binding protein 20; 20 kDa nuclear cap-binding protein, NCBP 20 kDa subunit, CBP20, NCBP-interacting protein 1, NIP1, Cell proliferation-inducing gene 55 protein 
    Chain C
    Description Importin subunit alpha-2 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 50780.1 
    Source Method genetically manipulated  
    Entity Name Importin alpha 1; Karyopherin subunit alpha-2, SRP1-alpha, RAG cohort protein 1 

     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A NCBP1_HUMAN B2R718     
    B NCBP2_HUMAN B2RE91     
    C IMA1_HUMAN B9EJD6     

    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
    184   Nuclear Transcribed MRNA Catabolic Process Nonsense Mediated Decay  The Nonsense Mediated Decay Pathway For Nuclear Transcribed Mrnas Degrades Mrnas in Which an Amino Acid Codon Has Changed to a Nonsense Codon; This Prevents the Translation of Such Mrnas Into Truncated and Potentially Harmful Proteins. 
    6370   7 Methylguanosine MRNA Capping  Addition of the 7 Methylguanosine Cap to the 5' End of a Nascent Messenger RNA Transcript. 
    6397   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. 
    6417   Regulation of Translation  Any Process That Modulates the Frequency Rate or Extent of the Chemical Reactions and Pathways Resulting in the Formation of Proteins by the Translation of Mrna. 
    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. 
    8380   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. 
    31047   Gene Silencing by RNA  Any Process in Which RNA Molecules Inactivate Expression of Target Genes. 
    51028   MRNA Transport  The Directed Movement of MRNA Messenger Ribonucleic Acid 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. 
    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). 
    Chain B
    GO ID   Ontology GO Term Definition
    184   Nuclear Transcribed MRNA Catabolic Process Nonsense Mediated Decay  The Nonsense Mediated Decay Pathway For Nuclear Transcribed Mrnas Degrades Mrnas in Which an Amino Acid Codon Has Changed to a Nonsense Codon; This Prevents the Translation of Such Mrnas Into Truncated and Potentially Harmful Proteins. 
    6370   7 Methylguanosine MRNA Capping  Addition of the 7 Methylguanosine Cap to the 5' End of a Nascent Messenger RNA Transcript. 
    6397   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. 
    6408   Snrna Export From Nucleus  The Directed Movement of Snrna From the Nucleus to the Cytoplasm. 
    6417   Regulation of Translation  Any Process That Modulates the Frequency Rate or Extent of the Chemical Reactions and Pathways Resulting in the Formation of Proteins by the Translation of Mrna. 
    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. 
    8380   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. 
    31047   Gene Silencing by RNA  Any Process in Which RNA Molecules Inactivate Expression of Target Genes. 
    46833   Positive Regulation of RNA Export From Nucleus  Any Process That Activates or Increases the Frequency Rate or Extent of Directed Movement of RNA From the Nucleus Into the Cytoplasm. 
    51028   MRNA Transport  The Directed Movement of MRNA Messenger Ribonucleic Acid 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. 
    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 Human
    Scientific Name Homo sapiens  
    Gene kpna2, rch1, srp1
    Host Scientific Name Escherichia coli  
    Host Strain Bl21(de3)
    Host Vector Type Plasmid
    Host Plasmid Name PET 30


    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene cbp20, ncbp2, pig55
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Strain Sf21
    Host Vector Type Baculovirus
    Host Plasmid Name pVL1393


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene cbp80, ncbp, ncbp1
    Host Common Name Fall Armyworm
    Host Scientific Name Spodoptera frugiperda  
    Host Strain Sf21
    Host Vector Type Baculovirus
    Host Plasmid Name pVL1393


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 3q29 22916     nuclear cap binding protein subunit 2, 20kDa NCBP2    
    9 9q34.1 4686     nuclear cap binding protein subunit 1, 80kDa NCBP1    
    17 17q24.2 3838     karyopherin alpha 2 (RAG cohort 1, importin alpha 1) KPNA2    

    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
    rs11554642 LS-SNP   dbSNP   A 19 R - > K Coil 31% (Intermediate) 9 100403097
    rs111406212 LS-SNP   dbSNP   A 29 D - > G Helix 64% (Exposed) 9 100403127
    rs199768033 LS-SNP   dbSNP   A 62 P - > R Helix 80% (Exposed) 9 100403905
    rs200044823 LS-SNP   dbSNP   A 90 V - > A Helix 0% (Buried) 9 100405530
    rs78263197 LS-SNP   dbSNP   A 106 E - > K Helix 52% (Exposed) 9 100405577
    rs201055450 LS-SNP   dbSNP   A 121 Y - > C Helix 4% (Buried) 9 100405623
    rs143745791 LS-SNP   dbSNP   A 125 V - > M Helix 5% (Buried) 9 100405634
    rs113188050 LS-SNP   dbSNP   A 132 S - > P Helix 0% (Buried) 9 100407411
    rs143244138 LS-SNP   dbSNP   A 138 H - > R Turn 22% (Intermediate) 9 100407430
    rs148430361 LS-SNP   dbSNP   A 154 S - > G 3/10 Helix 40% (Exposed) 9 100407477
    rs146735643 LS-SNP   dbSNP   A 155 V - > A 3/10 Helix 0% (Buried) 9 100407481
    rs199742053 LS-SNP   dbSNP   A 155 V - > I 3/10 Helix 0% (Buried) 9 100407480
    rs144152800 LS-SNP   dbSNP   A 194 R - > C Helix 56% (Exposed) 9 100407983
    rs146305083 LS-SNP   dbSNP   A 219 A - > S Coil 24% (Intermediate) 9 100409817
    rs145175516 LS-SNP   dbSNP   A 317 N - > S Helix 14% (Intermediate) 9 100412837
    rs77021424 LS-SNP   dbSNP   A 338 S - > N Bend 58% (Exposed) 9 100413609
    rs146487190 LS-SNP   dbSNP   A 352 V - > I Helix 0% (Buried) 9 100413650
    rs201033807 LS-SNP   dbSNP   A 364 A - > V Coil 45% (Exposed) 9 100416111
    rs201715578 LS-SNP   dbSNP   A 400 M - > L Helix 46% (Exposed) 9 100417189
    rs191669699 LS-SNP   dbSNP   A 401 R - > H Turn 19% (Intermediate) 9 100417193
    rs77602722 LS-SNP   dbSNP   A 446 P - > L Helix 1% (Buried) 9 100418331
    rs112377432 LS-SNP   dbSNP   A 494 S - > P Turn 94% (Exposed) 9 100423230
    rs141653335 LS-SNP   dbSNP   A 544 I - > T Helix 1% (Buried) 9 100424354
    rs200307901 LS-SNP   dbSNP   A 596 N - > K Turn 34% (Intermediate) 9 100425320
    rs189780807 LS-SNP   dbSNP   A 610 R - > H Turn 33% (Intermediate) 9 100426653
    rs199656608 LS-SNP   dbSNP   A 630 R - > C Bend 74% (Exposed) 9 100426712
    rs76139042 LS-SNP   dbSNP   A 630 R - > H Bend 74% (Exposed) 9 100426713
    rs35694910 LS-SNP   dbSNP   A 657 K - > Q Helix 56% (Exposed) 9 100429112
    rs201932796 LS-SNP   dbSNP   A 727 R - > G Helix 43% (Exposed) 9 100431908
    rs148698789 LS-SNP   dbSNP   A 739 W - > R Helix 29% (Intermediate) 9 100431944
    rs142212526 LS-SNP   dbSNP   A 776 P - > T Helix 68% (Exposed) 9 100433434
    rs139000685 LS-SNP   dbSNP   B 52 T - > P Coil 46% (Exposed) 3 196666228
    rs139792733 LS-SNP   dbSNP   C 69 N - > K Coil 126% (Exposed) 17 66033605
    rs142064368 LS-SNP   dbSNP   C 86 N - > S Coil 86% (Exposed) 17 66036837
    rs148032855 LS-SNP   dbSNP   C 117 R - > Q Turn 74% (Exposed) 17 66038248
    rs144637470 LS-SNP   dbSNP   C 117 R - > W Turn 74% (Exposed) 17 66038247
    rs200993285 LS-SNP   dbSNP   C 134 S - > G Helix 18% (Intermediate) 17 66038298
    rs142601381 LS-SNP   dbSNP   C 155 T - > S Helix 0% (Buried) 17 66038362
    rs17850032 LS-SNP   dbSNP   C 157 A - > V Helix 26% (Intermediate) 17 66038368
    rs11545989 LS-SNP   dbSNP   C 165 P - > R Helix 36% (Exposed) 17 66038392
    rs200169734 LS-SNP   dbSNP   C 205 A - > V Coil 0% (Buried) 17 66039063
    rs200624474 LS-SNP   dbSNP   C 236 L - > P Turn 2% (Buried) 17 66039256
    rs146139322 LS-SNP   dbSNP   C 244 P - > T Coil 6% (Buried) 17 66039279
    rs11545987 LS-SNP   dbSNP   C 244 P - > L Coil 6% (Buried) 17 66039280
    rs141613156 LS-SNP   dbSNP   C 255 T - > I Helix 10% (Intermediate) 17 66039313
    rs140011802 LS-SNP   dbSNP   C 255 T - > S Helix 10% (Intermediate) 17 66039312
    rs148427582 LS-SNP   dbSNP   C 296 P - > H Helix 57% (Exposed) 17 66039436
    rs200362872 LS-SNP   dbSNP   C 311 T - > I Helix 28% (Intermediate) 17 66039955
    rs145172573 LS-SNP   dbSNP   C 336 A - > V 3/10 Helix 2% (Buried) 17 66040030
    rs138064111 LS-SNP   dbSNP   C 356 T - > M Helix 0% (Buried) 17 66040090
    rs1059558 LS-SNP   dbSNP   C 365 G - > S Bend 6% (Buried) 17 66040116
    rs202041693 LS-SNP   dbSNP   C 366 R - > C Coil 37% (Exposed) 17 66040119
    rs147590540 LS-SNP   dbSNP   C 373 V - > L Helix 0% (Buried) 17 66040140
    rs140456943 LS-SNP   dbSNP   C 373 V - > D Helix 0% (Buried) 17 66040141
    rs1136738 LS-SNP   dbSNP   C 385 V - > D Helix 6% (Buried) 17 66040177
    rs112072422 LS-SNP   dbSNP   C 388 K - > E Turn 86% (Exposed) 17 66040185
    rs3208857 LS-SNP   dbSNP   C 390 D - > V Coil 50% (Exposed) 17 66040441
    rs1136737 LS-SNP   dbSNP   C 392 K - > E Helix 48% (Exposed) 17 66040446
    rs140410852 LS-SNP   dbSNP   C 418 H - > R Helix 88% (Exposed) 17 66040525
    rs1059538 LS-SNP   dbSNP   C 430 T - > P Turn 65% (Exposed) 17 66040560
    rs17850031 LS-SNP   dbSNP   C 453 K - > N Turn 74% (Exposed) 17 66041899
    rs145733510 LS-SNP   dbSNP   C 458 E - > G Helix 66% (Exposed) 17 66041913
    rs148952966 LS-SNP   dbSNP   C 462 I - > L Helix 52% (Exposed) 17 66041924
    rs1802812 LS-SNP   dbSNP   C 470 L - > V Helix 16% (Intermediate) 17 66041948