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Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4
Biology and Chemistry Report
4H9P
  •   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 G90A, S96A, Y99F, G102A, A111T, M120F 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 15272.0 
    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
    6336   DNA Replication Independent Nucleosome Assembly  The Formation of Nucleosomes Outside the Context of DNA Replication. 
    7596   Blood Coagulation  The Sequential Process in Which the Multiple Coagulation Factors of the Blood Interact Ultimately Resulting in the Formation of an Insoluble Fibrin Clot; It May Be Divided Into Three Stages: Stage 1 the Formation of Intrinsic and Extrinsic Prothrombin Converting Principle; Stage 2 the Formation of Thrombin; Stage 3 the Formation of Stable Fibrin Polymers. 
    30307   Positive Regulation of Cell Growth  Any Process That Activates or Increases the Frequency Rate Extent or Direction of Cell Growth. 
    228   Nuclear Chromosome  A Chromosome Found in the Nucleus of a Eukaryotic Cell. 
    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. 
    788   Nuclear Nucleosome  A Complex Comprised of DNA Wound Around a Multisubunit Core and Associated Proteins Which Forms the Primary Packing Unit of DNA in the Nucleus Into Higher Order Structures. 
    5576   Extracellular Region  The Space External to the Outermost Structure of a Cell. For Cells Without External Protective or External Encapsulating Structures This Refers to Space Outside of the Plasma Membrane. This Term Covers the Host Cell Environment Outside an Intracellular Parasite. 
    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. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5694   Chromosome  A Structure Composed of a Very Long Molecule of DNA and Associated Proteins (e.g. Histones) That Carries Hereditary Information. 
    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. 
    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. 
    979   RNA Polymerase Ii Core Promoter Sequence Specific DNA Binding  Interacting Selectively and Non Covalently with the Regulatory Region Composed of the Transcription Start Site and Binding Sites For Transcription Factors of the RNA Polymerase Ii Basal Transcription Machinery. 
    980   RNA Polymerase Ii Distal Enhancer Sequence Specific DNA Binding  Interacting Selectively and Non Covalently with a RNA Polymerase Ii (pol Ii) Distal Enhancer. in Mammalian Cells Enhancers Are Distal Sequences That Increase the Utilization of Some Promoters and Can Function in Either Orientation and in Any Location (upstream or Downstream) Relative to the Core Promoter. 
    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). 
    31492   Nucleosomal DNA Binding  Interacting Selectively and Non Covalently with the DNA Portion of a Nucleosome. 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    Chain B
    GO ID   Ontology GO Term Definition
    278   Mitotic Cell Cycle  Progression Through the Phases of the Mitotic Cell Cycle the Most Common Eukaryotic Cell Cycle Which Canonically Comprises Four Successive Phases Called G1 S G2 and M and Includes Replication of the Genome and the Subsequent Segregation of Chromosomes Into Daughter Cells. in Some Variant Cell Cycles Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division or G1 and G2 Phases May Be Absent. 
    723   Telomere Maintenance  Any Process That Contributes to the Maintenance of Proper Telomeric Length and Structure by Affecting and Monitoring the Activity of Telomeric Proteins and the Length of Telomeric Dna. These Processes Includes Those That Shorten and Lengthen the Telomeric DNA Sequences. 
    6325   Chromatin Organization  Any Process That Results in the Specification Formation or Maintenance of the Physical Structure of Eukaryotic Chromatin. 
    6334   Nucleosome Assembly  The Aggregation Arrangement and Bonding Together of a Nucleosome the Beadlike Structural Units of Eukaryotic Chromatin Composed of Histones and Dna. 
    6335   DNA Replication Dependent Nucleosome Assembly  The Formation of Nucleosomes On Newly Replicated DNA Coupled to Strand Elongation. 
    6336   DNA Replication Independent Nucleosome Assembly  The Formation of Nucleosomes Outside the Context of DNA Replication. 
    6352   DNA Templated Transcription Initiation  Any Process Involved in the Assembly of the RNA Polymerase Preinitiation Complex (pic) At the Core Promoter Region of a DNA Template Resulting in the Subsequent Synthesis of RNA From That Promoter. the Initiation Phase Includes Pic Assembly and the Formation of the First Few Bonds in the RNA Chain Including Abortive Initiation Which Occurs When the First Few Nucleotides Are Repeatedly Synthesized and Then Released. the Initiation Phase Ends Just Before and Does Not Include Promoter Clearance or Release Which Is the Transition Between the Initiation and Elongation Phases of Transcription. 
    34080   Cenp a Containing Nucleosome Assembly  The Formation of Nucleosomes Containing the Histone H3 Variant Cenp a to Form Centromeric Chromatin. This Specialised Chromatin Occurs At Centromeric Region in Point Centromeres and the Central Core in Modular Centromeres. 
    35574   Histone H4 K20 Demethylation  The Modification of Histone H4 by the Removal of a Methyl Group From Lysine At Position 20 of the Histone. 
    45653   Negative Regulation of Megakaryocyte Differentiation  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Megakaryocyte Differentiation. 
    228   Nuclear Chromosome  A Chromosome Found in the Nucleus of a Eukaryotic Cell. 
    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. 
    5576   Extracellular Region  The Space External to the Outermost Structure of a Cell. For Cells Without External Protective or External Encapsulating Structures This Refers to Space Outside of the Plasma Membrane. This Term Covers the Host Cell Environment Outside an Intracellular Parasite. 
    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. 
    5654   Nucleoplasm  That Part of the Nuclear Content Other Than the Chromosomes or the Nucleolus. 
    5694   Chromosome  A Structure Composed of a Very Long Molecule of DNA and Associated Proteins (e.g. Histones) That Carries Hereditary Information. 
    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. 
    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. 
    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. 
    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). 
    35575   Histone Demethylase Activity (h4 K20 Specific)  Catalysis of the Reaction: Histone H4 N6 Methyl L Lysine (position 20) + 2 Oxoglutarate + O2 = Histone H4 L Lysine (position 20) + Succinate + Formaldehyde + Co2. This Reaction Is the Removal of a Methyl Group From Lysine At Position 20 of the Histone H4 Protein. 
    44822   Poly(a) RNA Binding  Interacting Non Covalently with a Poly(a) RNA a RNA Molecule Which Has a Tail of Adenine Bases. 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 


     
  •   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 36% (Exposed) 17 73775134 PO4
    rs1803734 LS-SNP   dbSNP   A 53 R - > C Helix 9% (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 76% (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 78% (Exposed) 1 226259113 PO4
    rs200441194 LS-SNP   dbSNP   B 20 K - > N Coil 72% (Exposed) 6 26189242
    rs143050720 LS-SNP   dbSNP   B 21 V - > L Coil 105% (Exposed) 6 27107151
    rs141965015 LS-SNP   dbSNP   B 27 Q - > L Bend 52% (Exposed) 6 27841206
    rs184771900 LS-SNP   dbSNP   B 28 G - > S Bend 38% (Exposed) 6 26104260
    rs148131091 LS-SNP   dbSNP   B 29 I - > T Bend 7% (Buried) 6 27841200
    rs202183795 LS-SNP   dbSNP   B 30 T - > A Coil 45% (Exposed) 6 26240744
    rs202049591 LS-SNP   dbSNP   B 31 K - > Q Helix 55% (Exposed) 6 26189211
    rs41266819 LS-SNP   dbSNP   B 31 K - > R Helix 55% (Exposed) 6 26240748
    rs201894000 LS-SNP   dbSNP   B 32 P - > L Helix 49% (Exposed) 6 26189207
    rs200478043 LS-SNP   dbSNP   B 33 A - > V Helix 7% (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 13% (Intermediate) 6 27841182
    rs141729612 LS-SNP   dbSNP   B 35 R - > C Helix 13% (Intermediate) 12 14923913
    rs201381816 LS-SNP   dbSNP   B 39 R - > W Helix 53% (Exposed) 6 26022024
    rs201318128 LS-SNP   dbSNP   B 52 E - > D Helix 35% (Intermediate) 6 26189146
    rs148045723 LS-SNP   dbSNP   B 52 E - > Q Helix 35% (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 5% (Buried) 6 26027318
    rs149158970 LS-SNP   dbSNP   B 54 T - > I Helix 5% (Buried) 6 26027317
    rs200159567 LS-SNP   dbSNP   B 55 R - > C Helix 18% (Intermediate) 6 27107253
    rs146739153 LS-SNP   dbSNP   B 55 R - > C Helix 18% (Intermediate) 6 26240819
    rs140361782 LS-SNP   dbSNP   B 56 G - > E Helix 20% (Intermediate) 6 27107257
    rs146790408 LS-SNP   dbSNP   B 56 G - > R Helix 20% (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 14% (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 46% (Exposed) 6 26205096
    rs11548889 LS-SNP   dbSNP   B 78 R - > H Coil 37% (Exposed) 6 26285492
    rs143300286 LS-SNP   dbSNP   B 78 R - > P Coil 37% (Exposed) 6 26022142
    rs150538742 LS-SNP   dbSNP   B 78 R - > L Coil 37% (Exposed) 6 26189069
    rs199872319 LS-SNP   dbSNP   B 78 R - > C Coil 37% (Exposed) 6 26285493
    rs116193614 LS-SNP   dbSNP   B 78 R - > H Coil 37% (Exposed) 6 27107323
    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 1% (Buried) 6 26022157
    rs189209822 LS-SNP   dbSNP   B 84 M - > K Helix 24% (Intermediate) 6 26205126
    rs145023904 LS-SNP   dbSNP   B 84 M - > T Helix 24% (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 1% (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 43% (Exposed) 6_qbl_hap6 4521112 PO4
    rs200273259 LS-SNP   dbSNP   C 251 R - > H Coil 3% (Buried) 6_qbl_hap6 4521049
    rs146083974 LS-SNP   dbSNP   C 270 R - > C Helix 11% (Intermediate) 6 33288744
    rs149590152 LS-SNP   dbSNP   C 277 K - > N Coil 62% (Exposed) 6 33288721
    rs202052797 LS-SNP   dbSNP   C 299 R - > Q Helix 70% (Exposed) 6_qbl_hap6 4520905 PO4
    rs138014437 LS-SNP   dbSNP   C 306 R - > Q Helix 67% (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 52% (Exposed) 6_qbl_hap6 4520582
    rs138962926 LS-SNP   dbSNP   C 360 R - > C Helix 54% (Exposed) 6 33288330
    rs201251336 LS-SNP   dbSNP   C 369 M - > T Helix 37% (Exposed) 6_qbl_hap6 4520551
    rs61737694 LS-SNP   dbSNP   C 375 V - > I Helix 8% (Buried) 6_qbl_hap6 4520534