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(-) Description

Title :  CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 BOUND TO DIMETHYL-LYSINE AND IN CHIMERA WITH HISTONE H3.3(28-34)
 
Authors :  H. Li, D. J. Patel
Date :  09 Oct 07  (Deposition) - 11 Dec 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Protein-Peptide Complex, Dimethyl-Lysine, Alternative Splicing, Chromatin Regulator, Dna-Binding, Metal-Binding, Nucleus, Repressor, Transcription, Transcription Regulation, Zinc, Zinc-Finger (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Li, W. Fischle, W. Wang, E. M. Duncan, L. Liang, S. Murakami-Ishibe, C. D. Allis, D. J. Patel
Structural Basis For Lower Lysine Methylation State-Specific Readout By Mbt Repeats Of L3Mbtl1 And An Engineered Phd Finger.
Mol. Cell V. 28 677 2007
PubMed-ID: 18042461  |  Reference-DOI: 10.1016/J.MOLCEL.2007.10.023
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LETHAL(3)MALIGNANT BRAIN TUMOR-LIKE PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX6P
    Expression System StrainROSETTA2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentREPEATES MBT-1, MBT-2, MBT-3;
RESIDUES 206-519
    GeneL3MBTL, KIAA0681, L3MBT
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymL3, MBT-LIKE, L3, MBT PROTEIN HOMOLOG, H-L3, MBT PROTEIN, H-L3, MBT, L3MBTL1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1CML2Mod. Amino Acid(2S)-2-{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}BUTANEDIOIC ACID
2MLY1Mod. ResidueN-DIMETHYL-LYSINE
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4PG41Ligand/IonTETRAETHYLENE GLYCOL
5SO41Ligand/IonSULFATE ION

(-) Sites  (0, 0)

(no "Site" information available for 2RHU)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RHU)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RHU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_051098I479MLMBL1_HUMANPolymorphism6017104AI479M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MBTPS51079 MBT repeat profile.LMBL1_HUMAN206-306
314-413
422-517
  3A:206-306
A:314-413
A:422-517

(-) Exons   (0, 0)

(no "Exon" information available for 2RHU)

(-) 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:325
 aligned with LMBL1_HUMAN | Q9Y468 from UniProtKB/Swiss-Prot  Length:752

    Alignment length:326
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524      
          LMBL1_HUMAN   205 CWSWESYLEEQKAITAPVSLFQDSQAVTHNKNGFKLGMKLEGIDPQHPSMYFILTVAEVCGYRLRLHFDGYSECHDFWVNANSPDIHPAGWFEKTGHKLQPPKGYKEEEFSWSQYLRSTRAQAAPKHLFVSQSHSPPPLGFQVGMKLEAVDRMNPSLVCVASVTDVVDSRFLVHFDNWDDTYDYWCDPSSPYIHPVGWCQKQGKPLTPPQDYPDPDNFCWEKYLEETGASAVPTWAFKVRPPHSFLVNMKLEAVDRRNPALIRVASVEDVEDHRIKIHFDGWSHGYDFWIDADHPDIHPAGWCSKTGHPLQPPLGPREPSSASPGG 530
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rhuA01 A:205-234,A:447-529   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2rhuA01 A:205-234,A:447-529  [code=2.30.30.160, no name defined]                     CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MBT-2rhuA01 A:453-519                                              ----------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MBT-2rhuA02 A:453-519                                              ----------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MBT-2rhuA03 A:453-519                                              ----------- Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhh....hhhhhhhhhhh...........eeeeee..eeeeeeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh.........hhhhhhhhhhhhhhh....hhhhh................eeeeee..eeeeeeeeeeeeee..eeeeee...hhhhheee......ee..hhhhhhh..ee......hhhhhhhhhhhhhhh....hhhhh............eeeee.......eeeeeeeee...eeeeee...hhhhheeee.....ee..hhhhhhh...........-....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M--------------------------------------------------- SAPs(SNPs)
                    PROSITE -MBT  PDB: A:206-306 UniProt: 206-306                                                                 -------MBT  PDB: A:314-413 UniProt: 314-413                                                                --------MBT  PDB: A:422-517 UniProt: 422-517                                                            ------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rhu A 205 SWSWESYLEEQKAITAPVSLFQDSQAVTHNKNGFKLGMKLEGIDPQHPSMYFILTVAEVCGYRLRLHFDGYSEcHDFWVNANSPDIHPAGWFEKTGHKLQPPKGYKEEEFSWSQYLRSTRAQAAPKHLFVSQSHSPPPLGFQVGMKLEAVDRMNPSLVCVASVTDVVDSRFLVHFDNWDDTYDYWCDPSSPYIHPVGWCQKQGKPLTPPQDYPDPDNFcWEKYLEETGASAVPTWAFKVRPPHSFLVNMKLEAVDRRNPALIRVASVEDVEDHRIKIHFDGWSHGYDFWIDADHPDIHPAGWCSKTGHPLQPPLGGGG-SAPSTGG 529
                                   214       224       234       244       254       264       274   |   284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       523      
                                                                                                   278-CML                                                                                                                                          423-CML                                                                                            522 |      
                                                                                                                                                                                                                                                                                                                                                         523      

   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 2RHU)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: Tudor (88)
(-)
Family: MBT (24)
1aMBT-2rhuA01A:453-519
1bMBT-2rhuA02A:453-519
1cMBT-2rhuA03A:453-519

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LMBL1_HUMAN | Q9Y468)
molecular function
    GO:0032093    SAM domain binding    Interacting selectively and non-covalently with a SAM (Sterile Alpha Motif) domain, which is a 70-amino acid protein sequence that participates in protein-protein, protein-lipid, and protein-RNA interactions and is conserved from lower to higher eukaryotes.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
    GO:0031493    nucleosomal histone binding    Interacting selectively and non-covalently with a histone that is assembled into a nucleosome.
    GO:0031491    nucleosome binding    Interacting selectively and non-covalently with a 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: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:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    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:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0045652    regulation of megakaryocyte differentiation    Any process that modulates the frequency, rate or extent of megakaryocyte differentiation.
    GO:0007088    regulation of mitotic nuclear division    Any process that modulates the frequency, rate or extent of mitosis.
    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:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    GO:0000793    condensed chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct structure.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LMBL1_HUMAN | Q9Y4681oyx 1oz2 1oz3 2pqw 2rhi 2rhx 2rhy 2rhz 2ri2 2ri3 2ri5 2rjc 2rjd 2rje 2rjf 3oq5 3p8h 3uwn

(-) Related Entries Specified in the PDB File

2rhi CRYSTAL STRUCTURE OF THE 3-MBT DOMAIN FROM HUMAN L3MBTL1 IN COMPLEX WITH H1.5K27ME2 AT 1.66 ANGSTROM
2rhx CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 BOUND TO DIMETHYL-LYSINE
2rhy CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 BOUND TO MONOMETHYL-LYSINE
2rhz CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 WITH D355N POINT MUTATION
2ri2 CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 WITH D355A POINT MUTATION
2ri3 CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 WITH N358Q POINT MUTATION
2ri5 CRYSTAL STRUCTURE OF THE 3-MBT REPEATS FROM HUMAN L3MBTL1 WITH N358A POINT MUTATION