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Complex structure 1 of DAXX/H3.3(sub5)/H4
Biology and Chemistry Report
4H9N
  •   Structure Details   Hide

    Structure Keywords

    Keywords DNA BINDING PROTEIN/APOPTOSIS
    Text histone chaperone, DNA BINDING PROTEIN-APOPTOSIS complex

    Polymeric Molecules

    Chain A
    Description Histone H3.3 
    Mutation S96A, Y99F, G102A, A111T, M120F 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 15258.0 
    Source Method genetically manipulated  
    Chain B
    Description Histone H4 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 11263.3 
    Source Method genetically manipulated  
    Chain C
    Description Death domain-associated protein 6 
    Fragment UNP residues 178-389 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 24725.5 
    Source Method genetically manipulated  
    Entity Name Daxx, hDaxx, ETS1-associated protein 1, EAP1, Fas death domain-associated protein 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    PO4  PHOSPHATE ION  O4 P   94.97  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A H33_HUMAN P06351     
    B H4_HUMAN A2VCL0     
    C DAXX_HUMAN B4E1I3     

    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
    786   Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA Into Higher Order Structures. 
    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. 
    5694   Chromosome  A Structure Composed of a Very Long Molecule of DNA and Associated Proteins (e.g. Histones) That Carries Hereditary Information. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    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
    786   Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA Into Higher Order Structures. 
    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. 
    5694   Chromosome  A Structure Composed of a Very Long Molecule of DNA and Associated Proteins (e.g. Histones) That Carries Hereditary Information. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    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 daxx, bing2, dap6
    Host Scientific Name Escherichia coli  


    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene hist1h4a, h4/a, h4fa, hist1h4b, h4/i, h4fi, hist1h4c, h4/g, h4fg, hist1h4d, h4/b, h4fb, hist1h4e, h4/j, h4fj, hist1h4f, h4/c, h4fc, hist1h4h, h4/h, h4fh, hist1h4i, h4/m, h4fm, hist1h4j, h4/e, h4fe, hist1h4k, h4/d, h4fd, hist1h4l, h4/k, h4fk, hist2h4a, h4/n, h4f2, h4fn, hist2h4, hist2h4b, h4/o, h4fo, hist4h4
    Host Scientific Name Escherichia coli  


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Gene h3f3a, h3.3a, h3f3, pp781, h3f3b, h3.3b
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    1 1q42.12 3020     H3 histone, family 3A H3F3A    
    1 1q21.2 8370     histone cluster 2, H4a HIST2H4A    
    1 1q21 554313     histone cluster 2, H4b HIST2H4B    
    6 6p21.33 8294     histone cluster 1, H4i HIST1H4I    
    6 6p22.1 8359     histone cluster 1, H4a HIST1H4A    
    6 6p22.1 8360     histone cluster 1, H4d HIST1H4D    
    6 6p22.1 8361     histone cluster 1, H4f HIST1H4F    
    6 6p22.1 8362     histone cluster 1, H4k HIST1H4K    
    6 6p22.1 8363     histone cluster 1, H4j HIST1H4J    
    6 6p22.1 8364     histone cluster 1, H4c HIST1H4C    
    6 6p22.1 8365     histone cluster 1, H4h HIST1H4H    
    6 6p22.1 8366     histone cluster 1, H4b HIST1H4B    
    6 6p22.1 8367     histone cluster 1, H4e HIST1H4E    
    6 6p22.1 8368     histone cluster 1, H4l HIST1H4L    
    6 6p21.3 1616     death-domain associated protein DAXX    
    12 12p12.3 121504     histone cluster 4, H4 HIST4H4    
    17 17q25.1 3021     H3 histone, family 3B (H3.3B) H3F3B    

    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
    rs11547396 LS-SNP   dbSNP   A 40 R - > H Coil 30% (Intermediate) 17 73775134 PO4
    rs1803734 LS-SNP   dbSNP   A 53 R - > C Helix 10% (Intermediate) 1 226253388
    rs11547388 LS-SNP   dbSNP   A 68 Q - > H Helix 0% (Buried) 17 73774966
    rs11547392 LS-SNP   dbSNP   A 77 D - > V Helix 73% (Exposed) 17 73774940
    rs4896 LS-SNP   dbSNP   A 92 L - > F Helix 0% (Buried) 1 226253507
    rs11544228 LS-SNP   dbSNP   A 96 S - > R Helix 0% (Buried) 1 226259060
    rs75447292 LS-SNP   dbSNP   A 114 A - > G Bend 68% (Exposed) 1 226259113 PO4
    rs200441194 LS-SNP   dbSNP   B 20 K - > N Coil 70% (Exposed) 6 26189242
    rs143050720 LS-SNP   dbSNP   B 21 V - > L Coil 104% (Exposed) 6 27107151
    rs141965015 LS-SNP   dbSNP   B 27 Q - > L Bend 49% (Exposed) 6 27841206
    rs184771900 LS-SNP   dbSNP   B 28 G - > S Bend 44% (Exposed) 6 26104260
    rs148131091 LS-SNP   dbSNP   B 29 I - > T Bend 10% (Intermediate) 6 27841200
    rs202183795 LS-SNP   dbSNP   B 30 T - > A Coil 27% (Intermediate) 6 26240744
    rs202049591 LS-SNP   dbSNP   B 31 K - > Q Helix 42% (Exposed) 6 26189211
    rs41266819 LS-SNP   dbSNP   B 31 K - > R Helix 42% (Exposed) 6 26240748
    rs201894000 LS-SNP   dbSNP   B 32 P - > L Helix 31% (Intermediate) 6 26189207
    rs200478043 LS-SNP   dbSNP   B 33 A - > V Helix 8% (Buried) 6 26027380
    rs181114978 LS-SNP   dbSNP   B 34 I - > L Helix 0% (Buried) 6 26285625
    rs200857174 LS-SNP   dbSNP   B 35 R - > L Helix 50% (Exposed) 6 27841182
    rs141729612 LS-SNP   dbSNP   B 35 R - > C Helix 50% (Exposed) 12 14923913
    rs201381816 LS-SNP   dbSNP   B 39 R - > W Helix 38% (Exposed) 6 26022024
    rs201318128 LS-SNP   dbSNP   B 52 E - > D Helix 32% (Intermediate) 6 26189146
    rs148045723 LS-SNP   dbSNP   B 52 E - > Q Helix 32% (Intermediate) 12 14923862
    rs147907725 LS-SNP   dbSNP   B 53 E - > D Helix 3% (Buried) 6 26027319
    rs148995564 LS-SNP   dbSNP   B 53 E - > K Helix 3% (Buried) 6 27841129
    rs143307191 LS-SNP   dbSNP   B 54 T - > A Helix 6% (Buried) 6 26027318
    rs149158970 LS-SNP   dbSNP   B 54 T - > I Helix 6% (Buried) 6 26027317
    rs200159567 LS-SNP   dbSNP   B 55 R - > C Helix 12% (Intermediate) 6 27107253
    rs146739153 LS-SNP   dbSNP   B 55 R - > C Helix 12% (Intermediate) 6 26240819
    rs140361782 LS-SNP   dbSNP   B 56 G - > E Helix 21% (Intermediate) 6 27107257
    rs146790408 LS-SNP   dbSNP   B 56 G - > R Helix 21% (Intermediate) 6 27841120
    rs201938912 LS-SNP   dbSNP   B 58 L - > R Helix 1% (Buried) 6 26027305
    rs202202685 LS-SNP   dbSNP   B 58 L - > F Helix 1% (Buried) 6 26027306
    rs139418296 LS-SNP   dbSNP   B 62 L - > R Helix 0% (Buried) 6 26027293
    rs139563717 LS-SNP   dbSNP   B 63 E - > K Helix 12% (Intermediate) 6 26027291
    rs149672595 LS-SNP   dbSNP   B 66 I - > T Helix 0% (Buried) 6 26189105
    rs141333633 LS-SNP   dbSNP   B 66 I - > T Helix 0% (Buried) 6 26205072
    rs201889588 LS-SNP   dbSNP   B 67 R - > S Helix 15% (Intermediate) 6 26205074
    rs200288965 LS-SNP   dbSNP   B 69 A - > T Helix 0% (Buried) 6 26205080
    rs199660178 LS-SNP   dbSNP   B 74 E - > G Helix 49% (Exposed) 6 26205096
    rs11548889 LS-SNP   dbSNP   B 78 R - > H Coil 36% (Intermediate) 6 26285492 PO4
    rs143300286 LS-SNP   dbSNP   B 78 R - > P Coil 36% (Intermediate) 6 26022142 PO4
    rs150538742 LS-SNP   dbSNP   B 78 R - > L Coil 36% (Intermediate) 6 26189069 PO4
    rs199872319 LS-SNP   dbSNP   B 78 R - > C Coil 36% (Intermediate) 6 26285493 PO4
    rs116193614 LS-SNP   dbSNP   B 78 R - > H Coil 36% (Intermediate) 6 27107323 PO4
    rs113909556 LS-SNP   dbSNP   B 81 V - > A Beta Ladder 0% (Buried) 6 27799061
    rs199857326 LS-SNP   dbSNP   B 81 V - > A Beta Ladder 0% (Buried) 6 26022151
    rs200327357 LS-SNP   dbSNP   B 82 T - > I Coil 13% (Intermediate) 6 26104423
    rs144742137 LS-SNP   dbSNP   B 82 T - > I Coil 13% (Intermediate) 6 26189057
    rs150504596 LS-SNP   dbSNP   B 82 T - > I Coil 13% (Intermediate) 6 26027233
    rs147105535 LS-SNP   dbSNP   B 83 A - > V Helix 2% (Buried) 6 26022157
    rs189209822 LS-SNP   dbSNP   B 84 M - > K Helix 23% (Intermediate) 6 26205126
    rs145023904 LS-SNP   dbSNP   B 84 M - > T Helix 23% (Intermediate) 6 27841035
    rs138088561 LS-SNP   dbSNP   B 85 D - > G Helix 2% (Buried) 6 27107344
    rs201833445 LS-SNP   dbSNP   B 85 D - > G Helix 2% (Buried) 6 27841032
    rs148427340 LS-SNP   dbSNP   B 89 A - > V Helix 0% (Buried) 6 26027212
    rs144469714 LS-SNP   dbSNP   B 89 A - > S Helix 0% (Buried) 6 26104443
    rs199563791 LS-SNP   dbSNP   B 91 K - > R Turn 25% (Intermediate) 6 26205147
    rs200412707 LS-SNP   dbSNP   B 92 R - > H Turn 30% (Intermediate) 6 27841011
    rs201947121 LS-SNP   dbSNP   B 92 R - > S Turn 30% (Intermediate) 6 27799029
    rs143646853 LS-SNP   dbSNP   B 97 L - > V Turn 0% (Buried) 6 27107379
    rs201783122 LS-SNP   dbSNP   B 100 F - > S Turn 8% (Buried) 12 14923717
    rs151068394 LS-SNP   dbSNP   B 102 G - > D Coil 100% (Exposed) 6 26240961
    rs45526033 LS-SNP   dbSNP   B 102 G - > S Coil 100% (Exposed) 6 27840982
    rs201985154 LS-SNP   dbSNP   C 230 R - > L Helix 36% (Exposed) 6_qbl_hap6 4521112 PO4
    rs200273259 LS-SNP   dbSNP   C 251 R - > H Coil 2% (Buried) 6_qbl_hap6 4521049
    rs146083974 LS-SNP   dbSNP   C 270 R - > C Helix 7% (Buried) 6 33288744
    rs149590152 LS-SNP   dbSNP   C 277 K - > N Coil 55% (Exposed) 6 33288721
    rs202052797 LS-SNP   dbSNP   C 299 R - > Q Helix 67% (Exposed) 6_qbl_hap6 4520905 PO4
    rs138014437 LS-SNP   dbSNP   C 306 R - > Q Helix 74% (Exposed) 6 33288635
    rs141322869 LS-SNP   dbSNP   C 353 S - > L 3/10 Helix 83% (Exposed) 6 33288350
    rs200104639 LS-SNP   dbSNP   C 359 R - > W Helix 35% (Intermediate) 6_qbl_hap6 4520582
    rs138962926 LS-SNP   dbSNP   C 360 R - > C Helix 53% (Exposed) 6 33288330
    rs201251336 LS-SNP   dbSNP   C 369 M - > T Helix 36% (Exposed) 6_qbl_hap6 4520551
    rs61737694 LS-SNP   dbSNP   C 375 V - > I Helix 8% (Buried) 6_qbl_hap6 4520534