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(-) Description

Title :  HUMAN MSL3 CHROMODOMAIN BOUND TO DNA AND H4K20ME1 PEPTIDE
 
Authors :  D. Kim, P. Huang, F. Rastinejad, S. Khorasanizadeh
Date :  04 Aug 10  (Deposition) - 18 Aug 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Chromodomain, Msl3, Histone H4 Tail, Dna Backbone Recognition, Methyllysine Recognition, H4K20Me1, Aromatic Cage, Msl Complex, Transcription Upregulation, Dna Binding Protein-Dna Complex, Dna Binding Protein, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kim, B. J. Blus, V. Chandra, P. Huang, F. Rastinejad, S. Khorasanizadeh
Corecognition Of Dna And A Methylated Histone Tail By The Msl3 Chromodomain.
Nat. Struct. Mol. Biol. V. 17 1027 2010
PubMed-ID: 20657587  |  Reference-DOI: 10.1038/NSMB.1856

(-) Compounds

Molecule 1 - MALE-SPECIFIC LETHAL 3 HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: CHROMODOMAIN
    Gene: MSL3, MSL3L1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MALE-SPECIFIC LETHAL-3 PROTEIN-LIKE 1, MSL3-LIKE 1, MALE- SPECIFIC LETHAL-3 HOMOLOG 1
 
Molecule 2 - DNA (5'-D(*GP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)- 3')
    Chains: C, E
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)- 3')
    Chains: D, F
    Engineered: YES
    Synthetic: YES
 
Molecule 4 - H4 PEPTIDE MONOMETHYLATED AT LYSINE 20
    Chains: G
    Engineered: YES
    Fragment: HISTONE H4
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEFG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1IMD1Ligand/IonIMIDAZOLE
2MLZ1Mod. Amino AcidN-METHYL-LYSINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP B:63 , HOH B:126BINDING SITE FOR RESIDUE IMD B 102

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OA6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3OA6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OA6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OA6)

(-) Exons   (0, 0)

(no "Exon" information available for 3OA6)

(-) 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:84
 aligned with MS3L1_HUMAN | Q8N5Y2 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:84
                                    18        28        38        48        58        68        78        88    
           MS3L1_HUMAN    9 FKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......eeeee.........eeeeeeeeeeeee.....eeeeeeeee...hhhhheeee...eee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3oa6 A  9 FKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
                                    18        28        38        48        58        68        78        88    


Chain B from PDB  Type:PROTEIN  Length:84
 aligned with MS3L1_HUMAN | Q8N5Y2 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:84
                                    18        28        38        48        58        68        78        88    
           MS3L1_HUMAN    9 FKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --Tudor-knot-3oa6B01 B:11-74                                      ------------------ Pfam domains (1)
           Pfam domains (2) --Tudor-knot-3oa6B02 B:11-74                                      ------------------ Pfam domains (2)
         Sec.struct. author .......eeeee.........eeeeeeeeeeeee.....eeeeeeeee...hhhhheeee...eee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                  3oa6 B  9 FKFHSGEKVLCFEPDPTKARVLYDAKIVDVIVGKDEKGRKIPEYLIHFNGWNRSWDRWAAEDHVLRDTDENRRLQRKLARKAVA 92
                                    18        28        38        48        58        68        78        88    


Chain C from PDB  Type:DNA  Length:16
                                               
                  3oa6 C  1 GCTAGGTCAAAGGTCA 16
                                    10      


Chain D from PDB  Type:DNA  Length:16
                                               
                  3oa6 D  1 CTGACCTTTGACCTAG 16
                                    10      


Chain E from PDB  Type:DNA  Length:16
                                               
                  3oa6 E  1 GCTAGGTCAAAGGTCA 16
                                    10      


Chain F from PDB  Type:DNA  Length:16
                                               
                  3oa6 F  1 CTGACCTTTGACCTAG 16
                                    10      


Chain G from PDB  Type:PROTEIN  Length:5
                                    
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                  3oa6 G 18 HRkVL 22
                              |  
                             20-MLZ
   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)
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  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 3OA6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OA6)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Tudor (88)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (MS3L1_HUMAN | Q8N5Y2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0035064    methylated histone binding    Interacting selectively and non-covalently with a histone in which a residue has been modified by methylation. Histones are any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes.
biological process
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
    GO:0043968    histone H2A acetylation    The modification of histone H2A by the addition of an acetyl group.
    GO:0043984    histone H4-K16 acetylation    The modification of histone H4 by the addition of an acetyl group to a lysine residue at position 16 of the histone.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    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:0072487    MSL complex    A histone acetyltransferase complex that catalyzes the acetylation of a histone H4 lysine residue at position 16. In human, it contains the catalytic subunit MOF, and MSL1, MSL2 and MSL3.
    GO:0035267    NuA4 histone acetyltransferase complex    A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60).
    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.

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 Related Entries

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        MS3L1_HUMAN | Q8N5Y2: 2y0n 3ob9

(-) Related Entries Specified in the PDB File

3m9q DROSOPHILA MSL3 CHROMODOMAIN