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(-) Description

Title :  THE EFFECT OF H3 K79 DIMETHYLATION AND H4 K20 TRIMETHYLATION ON NUCLEOSOME AND CHROMATIN STRUCTURE
 
Authors :  X. Lu, M. Simon, J. Chodaparambil, J. Hansen, K. Shokat, K. Luger
Date :  22 Jan 08  (Deposition) - 07 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.15
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Nucleosome, Chromatin, Histone H3, Trimethylation, Histone Modification, Nucleosomal Surface, Nucleosomal Array, Acetylation, Chromosomal Protein, Dna-Binding, Methylation, Nucleosome Core, Nucleus, Phosphoprotein, Ubl Conjugation, Structural Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  X. Lu, M. D. Simon, J. V. Chodaparambil, J. C. Hansen, K. M. Shokat, K. Luger
The Effect Of H3K79 Dimethylation And H4K20 Trimethylation On Nucleosome And Chromatin Structure.
Nat. Struct. Mol. Biol. V. 15 1122 2008
PubMed-ID: 18794842  |  Reference-DOI: 10.1038/NSMB.1489
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE H3-LIKE
    ChainsA, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    GeneHISTONE H3
    Organism CommonCLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
 
Molecule 2 - HISTONE H4
    ChainsB, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    GeneHISTONE H4
    Organism CommonCLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
 
Molecule 3 - HISTONE H2A TYPE 1
    ChainsC, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    GeneHISTONE H2A
    Organism CommonCLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
 
Molecule 4 - HISTONE 2, H2BF
    ChainsD, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    GeneHIST2H2BF, TGAS058P09.1-001
    Organism CommonWESTERN CLAWED FROG
    Organism ScientificXENOPUS (SILURANA) TROPICALIS
    Organism Taxid8364
 
Molecule 5 - PALINDROMIC 146BP HUMAN ALPHA SATELLITE DNA
    ChainsI, J
    EngineeredYES
    Other DetailsSYNTHETIC DNA
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1M2L2Mod. Amino Acid(2R)-2-AMINO-3-(2-DIMETHYLAMINOETHYLSULFANYL)PROPANOIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 3C1C)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C1C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C1C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C1C)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H2APS00046 Histone H2A signature.H2A1_XENLA22-28
 
  2C:821-827
G:1021-1027
2HISTONE_H3_2PS00959 Histone H3 signature 2.H3C_XENLA67-75
 
  2A:466-474
E:666-674
H32_XENLA67-75
 
  2A:466-474
E:666-674

(-) Exons   (0, 0)

(no "Exon" information available for 3C1C)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:98
 aligned with H32_XENLA | P84233 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:98
                                    48        58        68        78        88        98       108       118       128        
           H32_XENLA     39 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA  136
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c1cA00 A:438-535 Histone, subunit A                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------HISTONE_H------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                3c1c A  438 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFkTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA  535
                                   447       457       467       477 |     487       497       507       517       527        
                                                                   479-M2L                                                    

Chain A from PDB  Type:PROTEIN  Length:98
 aligned with H3C_XENLA | P02302 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:98
                                    48        58        68        78        88        98       108       118       128        
           H3C_XENLA     39 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQRSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA  136
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c1cA00 A:438-535 Histone, subunit A                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------HISTONE_H------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                3c1c A  438 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFkTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGERA  535
                                   447       457       467       477 |     487       497       507       517       527        
                                                                   479-M2L                                                    

Chain B from PDB  Type:PROTEIN  Length:78
 aligned with H4_XENLA | P62799 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:78
                                    35        45        55        65        75        85        95        
            H4_XENLA     26 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG  103
               SCOP domains d3c1cb1 B:25-102 Histone H4                                                    SCOP domains
               CATH domains 3c1cB00 B:25-102 Histone, subunit A                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                3c1c B   25 NIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG  102
                                    34        44        54        64        74        84        94        

Chain C from PDB  Type:PROTEIN  Length:105
 aligned with H2A1_XENLA | P06897 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:105
                                    24        34        44        54        64        74        84        94       104       114     
          H2A1_XENLA     15 AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPK  119
               SCOP domains d3c1cc1 C:814-918 Histone H2A                                                                             SCOP domains
               CATH domains 3c1cC00 C:814-918 Histone, subunit A                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...hhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh...ee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------HISTONE------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                3c1c C  814 AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK  918
                                   823       833       843       853       863       873       883       893       903       913     

Chain D from PDB  Type:PROTEIN  Length:93
 aligned with Q28D68_XENTR | Q28D68 from UniProtKB/TrEMBL  Length:126

    Alignment length:93
                                    43        53        63        73        83        93       103       113       123   
        Q28D68_XENTR     34 RKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK  126
               SCOP domains d3c1cd1 D:1230-1322 Histone H2B                                                               SCOP domains
               CATH domains 3c1cD00 D:1230-1322 Histone, subunit A                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                3c1c D 1230 RKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 1322
                                  1239      1249      1259      1269      1279      1289      1299      1309      1319   

Chain E from PDB  Type:PROTEIN  Length:97
 aligned with H32_XENLA | P84233 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:97
                                    48        58        68        78        88        98       108       118       128       
           H32_XENLA     39 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER  135
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c1cE00 E:638-734 Histone, subunit A                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------------------------HISTONE_H------------------------------------------------------------ PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                3c1c E  638 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFkTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGER  734
                                   647       657       667       677 |     687       697       707       717       727       
                                                                   679-M2L                                                   

Chain E from PDB  Type:PROTEIN  Length:97
 aligned with H3C_XENLA | P02302 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:97
                                    48        58        68        78        88        98       108       118       128       
           H3C_XENLA     39 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQRSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGER  135
               SCOP domains ------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3c1cE00 E:638-734 Histone, subunit A                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------HISTONE_H------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------- Transcript
                3c1c E  638 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFkTDLRFQSSAVMALQEASEAYLVALFEDTNLAAIHAKRVTIMPKDIQLARRIRGER  734
                                   647       657       667       677 |     687       697       707       717       727       
                                                                   679-M2L                                                   

Chain F from PDB  Type:PROTEIN  Length:84
 aligned with H4_XENLA | P62799 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:84
                                    29        39        49        59        69        79        89        99    
            H4_XENLA     20 RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG  103
               SCOP domains -----d3c1cf1 F:224-302 Histone H4                                                    SCOP domains
               CATH domains 3c1cF00 F:219-302 Histone, subunit A                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhh.hhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                3c1c F  219 RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG  302
                                   228       238       248       258       268       278       288       298    

Chain G from PDB  Type:PROTEIN  Length:104
 aligned with H2A1_XENLA | P06897 from UniProtKB/Swiss-Prot  Length:130

    Alignment length:104
                                    26        36        46        56        66        76        86        96       106       116    
          H2A1_XENLA     17 TRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGGVTIAQGGVLPNIQSVLLPKK  120
               SCOP domains d3c1cg1 G:1016-1118 Histone H2A                                                                        - SCOP domains
               CATH domains 3c1cG00 G:1016-1119 Histone, subunit A                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....hhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eehhhhhhhhhh.hhhhhhhh...ee.........hhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----HISTONE-------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                3c1c G 1016 TRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK 1119
                                  1025      1035      1045      1055      1065      1075      1085      1095      1105      1115    

Chain H from PDB  Type:PROTEIN  Length:92
 aligned with Q28D68_XENTR | Q28D68 from UniProtKB/TrEMBL  Length:126

    Alignment length:92
                                    42        52        62        72        82        92       102       112       122  
        Q28D68_XENTR     33 TRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS  124
               SCOP domains d3c1ch1 H:1429-1520 Histone H2B                                                              SCOP domains
               CATH domains 3c1cH00 H:1429-1520 Histone, subunit A                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                3c1c H 1429 TRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 1520
                                  1438      1448      1458      1468      1478      1488      1498      1508      1518  

Chain I from PDB  Type:DNA  Length:146
                                                                                                                                                                                   
                3c1c I    1 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT  146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      

Chain J from PDB  Type:DNA  Length:146
                                                                                                                                                                                   
                3c1c J  147 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT  292
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286      

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (3, 6)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 8)

Asymmetric/Biological Unit

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C1C)

(-) Gene Ontology  (10, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,E   (H3C_XENLA | P02302)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000786    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.
    GO:0005634    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.

Chain A,E   (H32_XENLA | P84233)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    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).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0000786    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.
    GO:0005634    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.

Chain B,F   (H4_XENLA | P62799)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    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).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0006352    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.
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000786    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.
    GO:0005634    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.

Chain C,G   (H2A1_XENLA | P06897)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000786    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.
    GO:0005634    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.

Chain D,H   (Q28D68_XENTR | Q28D68)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000788    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.
    GO:0000786    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.
    GO:0005634    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        H2A1_XENLA | P068971aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2fj7 2nzd 3b6f 3b6g 3c1b 3kuy 3kwq 3lja 3mnn 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4j8u 4j8v 4j8w 4j8x 4ld9 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5e5a 5f99 5g2e 5hq2 5mlu 5nl0
        H32_XENLA | P842331f66 1kx3 1kx4 1kx5 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3gv6 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5f99 5hq2 5kgf 5mlu 5nl0 5x0x 5x0y
        H3C_XENLA | P023021aoi 1m18 1m19 1m1a 3c1b
        H4_XENLA | P627991aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zbj 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5e5a 5f99 5hq2 5kgf 5mlu 5nl0 5x0x 5x0y
UniProtKB/TrEMBL
        Q28D68_XENTR | Q28D683c1b

(-) Related Entries Specified in the PDB File

1aoi 1f66 1kx3 1kx4 1kx5 1zla 3c1b