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(-) Description

Title :  STRUCTURAL INSIGHTS INTO LYSINE MULTIPLE METHYLATION BY SET DOMAIN METHYLTRANSFERASES, SET8-Y334F / H4-LYS20ME2 / ADOHCY
 
Authors :  J-F. Couture, L. M. A. Dirk, J. S. Brunzelle, R. L. Houtz, R. C. Trievel
Date :  14 Nov 08  (Deposition) - 25 Nov 08  (Release) - 09 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Methyltransferase, Histone, Set, Lysine, Alternative Splicing, Cell Cycle, Cell Division, Chromatin Regulator, Chromosomal Protein, Coiled Coil, Mitosis, Nucleus, Repressor, S-Adenosyl-L-Methionine, Transcription, Transcription Regulation, Acetylation, Dna-Binding, Methylation, Nucleosome Core (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. F. Couture, L. M. Dirk, J. S. Brunzelle, R. L. Houtz, R. C. Trievel
Structural Origins For The Product Specificity Of Set Domain Protein Methyltransferases.
Proc. Natl. Acad. Sci. Usa V. 105 20659 2008
PubMed-ID: 19088188  |  Reference-DOI: 10.1073/PNAS.0806712105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD8
    ChainsA, B, C, D
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHIS2
    Expression System StrainBL21
    Expression System VectorPARALLEL
    Expression System Vector TypePLASMID
    FragmentSET DOMAIN: UNP RESIDUES 232-393
    GeneSETD8, KMT5A, PRSET7, SET07, SET8
    MutationYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymH4-K20-HMTASE SETD8, SET DOMAIN-CONTAINING PROTEIN 8, PR/SET DOMAIN-CONTAINING PROTEIN 07, PR/SET07, PR-SET7, LYSINE N-METHYLTRANSFERASE 5A
 
Molecule 2 - HISTONE H4
    ChainsE, F, G, H
    EngineeredYES
    FragmentUNP RESIDUES 16-25
    Other DetailsSYNTHETIC PEPTIDE CORRESPONDING TO RESIDUES 16-25 OF HUMAN HISTONE H4
    SyntheticYES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDEFGH
Biological Unit 1 (1x)A    F  
Biological Unit 2 (1x) B  E   
Biological Unit 3 (1x)  C   G 
Biological Unit 4 (1x)   D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1MLY4Mod. Amino AcidN-DIMETHYL-LYSINE
2SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1MLY1Mod. Amino AcidN-DIMETHYL-LYSINE
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:163 , HOH A:174 , GLY A:225 , LYS A:226 , ARG A:228 , TYR A:271 , ARG A:295 , LEU A:296 , ASN A:298 , HIS A:299 , TYR A:336 , TRP A:349 , HOH A:380 , HOH A:383 , HOH A:397 , HOH A:466 , HIS F:18 , MLY F:20BINDING SITE FOR RESIDUE SAH A 801
2AC2SOFTWAREHOH B:110 , GLY B:225 , LYS B:226 , ARG B:228 , TYR B:271 , ARG B:295 , LEU B:296 , ASN B:298 , HIS B:299 , TYR B:336 , TRP B:349 , HOH B:372 , HOH B:398 , HIS E:18 , MLY E:20BINDING SITE FOR RESIDUE SAH B 801
3AC3SOFTWAREGLY C:225 , LYS C:226 , ARG C:228 , TYR C:271 , ARG C:295 , LEU C:296 , ASN C:298 , HIS C:299 , TYR C:336 , TRP C:349 , HOH C:356 , HOH C:367 , HOH C:379 , HOH C:757 , HIS G:18BINDING SITE FOR RESIDUE SAH C 801
4AC4SOFTWAREHOH B:25 , HOH D:19 , HOH D:56 , GLY D:225 , LYS D:226 , ARG D:228 , TYR D:271 , ARG D:295 , LEU D:296 , ASN D:298 , HIS D:299 , TYR D:336 , TRP D:349 , HOH D:362 , HOH D:387 , HOH D:391 , ARG E:23 , HIS H:18 , MLY H:20BINDING SITE FOR RESIDUE SAH D 801

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3F9X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3F9X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3F9X)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5A_HUMAN257-378
 
 
 
  4A:216-337
B:216-337
C:216-337
D:216-337
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5A_HUMAN257-378
 
 
 
  1A:216-337
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5A_HUMAN257-378
 
 
 
  1-
B:216-337
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5A_HUMAN257-378
 
 
 
  1-
-
C:216-337
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.KMT5A_HUMAN257-378
 
 
 
  1-
-
-
D:216-337

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003778031ENSE00001475159chr6:26104104-26104518415H4_HUMAN1-1271274E:16-24
F:16-23
G:16-24
H:16-23
9
8
9
8

(-) Sequences/Alignments

Asymmetric 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:160
 aligned with KMT5A_HUMAN | Q9NQR1 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:160
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
          KMT5A_HUMAN   234 KSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH 393
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeee...eeeehhhhhhhhhhhh........eeeeee..eeeeee.......hhhhhee.....eeeeeeee..eeeeeeee..........ee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------SET  PDB: A:216-337 UniProt: 257-378                                                                                      --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f9x A 193 KSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLFDYGDRSKASIEAHPWLKH 352
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with KMT5A_HUMAN | Q9NQR1 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:160
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
          KMT5A_HUMAN   234 KSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH 393
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeee...eeeehhhhhhhhhhhh........eeeeee..eeeeee.......hhhhhee.....eeeeeeee..eeeeeeee..........ee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------SET  PDB: B:216-337 UniProt: 257-378                                                                                      --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f9x B 193 KSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLFDYGDRSKASIEAHPWLKH 352
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

Chain C from PDB  Type:PROTEIN  Length:160
 aligned with KMT5A_HUMAN | Q9NQR1 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:160
                                   243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
          KMT5A_HUMAN   234 KSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH 393
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeee...eeeehhhhhhhhhhhh........eeeeee..eeeeee.......hhhhhee.....eeeeeeee..eeeeeeee..........ee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------SET  PDB: C:216-337 UniProt: 257-378                                                                                      --------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f9x C 193 KSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLFDYGDRSKASIEAHPWLKH 352
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352

Chain D from PDB  Type:PROTEIN  Length:161
 aligned with KMT5A_HUMAN | Q9NQR1 from UniProtKB/Swiss-Prot  Length:393

    Alignment length:161
                                   242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392 
          KMT5A_HUMAN   233 RKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLYDYGDRSKASIEAHPWLKH 393
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh....eeeeee...eeeeee........eeeee..eeeehhhhhhhhhhhhhhhhhh..eeeeee..eeeeee.......hhhhhee.....eeeeeeee..eeeeeeee..........ee.....hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------SET  PDB: D:216-337 UniProt: 257-378                                                                                      --------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f9x D 192 RKSKAELQSEERKRIDELIESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGCYMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGEELLFDYGDRSKASIEAHPWLKH 352
                                   201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351 

Chain E from PDB  Type:PROTEIN  Length:9
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:9
             H4_HUMAN    17 KRHRKVLRD  25
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ....eee.. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
               Transcript 1 Exon 1.1  Transcript 1
                 3f9x E  16 KRHRkVLRD  24
                                |    
                                |    
                               20-MLY

Chain F from PDB  Type:PROTEIN  Length:8
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:8
             H4_HUMAN    17 KRHRKVLR  24
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ....ee.. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
               Transcript 1 Exon 1.1 Transcript 1
                 3f9x F  16 KRHRkVLR  23
                                |   
                               20-MLY

Chain G from PDB  Type:PROTEIN  Length:9
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:9
             H4_HUMAN    17 KRHRKVLRD  25
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ....ee... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
               Transcript 1 Exon 1.1  Transcript 1
                 3f9x G  16 KRHRkVLRD  24
                                |    
                               20-MLY

Chain H from PDB  Type:PROTEIN  Length:8
 aligned with H4_HUMAN | P62805 from UniProtKB/Swiss-Prot  Length:103

    Alignment length:8
             H4_HUMAN    17 KRHRKVLR  24
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ....ee.. Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
               Transcript 1 Exon 1.1 Transcript 1
                 3f9x H  16 KRHRkVLR  23
                                |   
                               20-MLY

   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  (0, 0)

(no "SCOP Domain" information available for 3F9X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3F9X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3F9X)

(-) Gene Ontology  (52, 56)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (KMT5A_HUMAN | Q9NQR1)
molecular function
    GO:0042799    histone methyltransferase activity (H4-K20 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H4 L-lysine (position 20) = S-adenosyl-L-homocysteine + histone H4 N6-methyl-L-lysine (position 20). This reaction is the addition of a methyl group onto lysine at position 20 of the histone H4 protein.
    GO:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0016278    lysine N-methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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:0016279    protein-lysine N-methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0007049    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.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0034770    histone H4-K20 methylation    The modification of histone H4 by addition of one or more methyl groups to lysine at position 20 of the histone.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0018026    peptidyl-lysine monomethylation    The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
    GO:0043516    regulation of DNA damage response, signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of the cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of 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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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 E,F,G,H   (H4_HUMAN | P62805)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0034080    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.
    GO:0006335    DNA replication-dependent nucleosome assembly    The formation of nucleosomes on newly replicated DNA, coupled to strand elongation.
    GO:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    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:1904837    beta-catenin-TCF complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0000183    chromatin silencing at rDNA    Repression of transcription of ribosomal DNA by altering the structure of chromatin.
    GO:0006303    double-strand break repair via nonhomologous end joining    The repair of a double-strand break in DNA in which the two broken ends are rejoined with little or no sequence complementarity. Information at the DNA ends may be lost due to the modification of broken DNA ends. This term covers instances of separate pathways, called classical (or canonical) and alternative nonhomologous end joining (C-NHEJ and A-NHEJ). These in turn may further branch into sub-pathways, but evidence is still unclear.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0045814    negative regulation of gene expression, epigenetic    Any epigenetic process that stops, prevents or reduces the rate of gene expression.
    GO:0045653    negative regulation of megakaryocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of megakaryocyte differentiation.
    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.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0051290    protein heterotetramerization    The formation of a protein heterotetramer, a macromolecular structure consisting of four noncovalently associated subunits, of which not all are identical.
    GO:0016233    telomere capping    A process in which telomeres are protected from degradation and fusion, thereby ensuring chromosome stability by protecting the ends from both degradation and from being recognized as damaged DNA. May be mediated by specific single- or double-stranded telomeric DNA binding proteins.
    GO:0032200    telomere organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of telomeres, terminal regions of a linear chromosome that include the telomeric DNA repeats and associated proteins.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000228    nuclear chromosome    A chromosome that encodes the nuclear genome and is found in the nucleus of a eukaryotic cell during the cell cycle phases when the nucleus is intact.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    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.
    GO:0043234    protein complex    A stable 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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        H4_HUMAN | P628051kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2lvm 2qqs 2rje 2rny 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4gqb 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4u9w 4ym5 4ym6 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5kdm 5teg 5x7x
        KMT5A_HUMAN | Q9NQR11zkk 2bqz 3f9w 3f9y 3f9z 4ij8 5hq2 5t5g 5teg 5th7 5w1y

(-) Related Entries Specified in the PDB File

1zkk CRYSTAL STRUCTURE OF HSET8 IN TERNARY COMPLEX WITH H4 PEPTIDE (16-24) AND ADOHCY
3f9w STRUCTURAL INSIGHTS INTO LYSINE MULTIPLE METHYLATION BY SET DOMAIN METHYLTRANSFERASES, SET8-Y334F / H4-LYS20 / ADOHCY
3f9y STRUCTURAL INSIGHTS INTO LYSINE MULTIPLE METHYLATION BY SET DOMAIN METHYLTRANSFERASES, SET8-Y334F / H4-LYS20ME1 / ADOHCY
3f9z STRUCTURAL INSIGHTS INTO LYSINE MULTIPLE METHYLATION BY SET DOMAIN METHYLTRANSFERASES, SET8-Y245F / H4-LYS20 / ADOHCY