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(-) Description

Title :  CRYSTAL STRUCTURE OF L3MBTL1 IN COMPLEX WITH H4K20ME2 (RESIDUES 17-25), TRIGONAL FORM
 
Authors :  A. Allali-Hassani, Y. Liu, N. Herzanych, H. Ouyang, F. Mackenzie, L. Cr P. Loppnau, I. Kozieradzki, M. Vedadi, J. Weigelt, M. Sundstrom, C. H. Arrowsmith, A. M. Edwards, A. Bochkarev, J. R. Min, Structural G Consortium (Sgc)
Date :  02 May 07  (Deposition) - 31 Jul 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  L(3)Mbt-Like Protein, Structural Genomics, Structural Genomics Consortium, Sgc, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Min, A. Allali-Hassani, N. Nady, C. Qi, H. Ouyang, Y. Liu, F. Mackenzie, M. Vedadi, C. H. Arrowsmith
L3Mbtl1 Recognition Of Mono- And Dimethylated Histones.
Nat. Struct. Mol. Biol. V. 14 1229 2007
PubMed-ID: 18026117  |  Reference-DOI: 10.1038/NSMB1340

(-) Compounds

Molecule 1 - LETHAL(3)MALIGNANT BRAIN TUMOR-LIKE PROTEIN
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28A-MHL
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 200-522
    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
 
Molecule 2 - HISTONE H4
    ChainsB
    EngineeredYES
    Other DetailsSYNTHETIC PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2MLY1Mod. Amino AcidN-DIMETHYL-LYSINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:293 , TRP A:316BINDING SITE FOR RESIDUE ACT A 523
2AC2SOFTWAREASP A:248 , PHE A:256BINDING SITE FOR RESIDUE ACT A 524
3AC3SOFTWARELYS A:243 , GLY A:348 , THR A:431 , HOH A:555 , HOH A:617BINDING SITE FOR RESIDUE ACT A 525

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 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 2PQW)

(-) 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:315
 aligned with LMBL1_HUMAN | Q9Y468 from UniProtKB/Swiss-Prot  Length:752

    Alignment length:315
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515     
          LMBL1_HUMAN   206 WSWESYLEEQKAITAPVSLFQDSQAVTHNKNGFKLGMKLEGIDPQHPSMYFILTVAEVCGYRLRLHFDGYSECHDFWVNANSPDIHPAGWFEKTGHKLQPPKGYKEEEFSWSQYLRSTRAQAAPKHLFVSQSHSPPPLGFQVGMKLEAVDRMNPSLVCVASVTDVVDSRFLVHFDNWDDTYDYWCDPSSPYIHPVGWCQKQGKPLTPPQDYPDPDNFCWEKYLEETGASAVPTWAFKVRPPHSFLVNMKLEAVDRRNPALIRVASVEDVEDHRIKIHFDGWSHGYDFWIDADHPDIHPAGWCSKTGHPLQPPLGP 520
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2pqwA01 A:206-234,A:447-520  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2pqwA01 A:206-234,A:447-520  [code=2.30.30.160, no name defined]           CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MBT-2pqwA01 A:453-520                                                Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MBT-2pqwA02 A:453-520                                                Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------MBT-2pqwA03 A:453-520                                                Pfam domains (3)
         Sec.struct. author .hhhhhhhhhh....hhhhhhhhhhh...........eeeeee..eeeeeeeeeeeeee..eeeeee...hhhhheeee.....ee..hhhhhhh..ee..........hhhhhhhhhh....hhhhh................eeeee.......eeeeeeeeee..eeeeee...hhhhheee......ee..hhhhhhh..ee......hhhhhhhhhhhhhh.....hhhhh............eeeee.......eeeeeeeee...eeeee....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
                 2pqw A 206 WSWESYLEEQKAITAPVSLFQDSQAVTHNKNGFKLGMKLEGIDPQHPSMYFILTVAEVCGYRLRLHFDGYSECHDFWVNANSPDIHPAGWFEKTGHKLQPPKGYKEEEFSWSQYLRSTRAQAAPKHLFVSQSHSPPPLGFQVGMKLEAVDRMNPSLVCVASVTDVVDSRFLVHFDNWDDTYDYWCDPSSPYIHPVGWCQKQGKPLTPPQDYPDPDNFCWEKYLEETGASAVPTWAFKVRPPHSFLVNMKLEAVDRRNPALIRVASVEDVEDHRIKIHFDGWSHGYDFWIDADHPDIHPAGWCSKTGHPLQPPLGP 520
                                   215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515     

Chain B from PDB  Type:PROTEIN  Length:9
                                         
               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
                 2pqw B  17 RHRkVLRDN  25
                               |     
                              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 2PQW)

(-) 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-2pqwA01A:453-520
1bMBT-2pqwA02A:453-520
1cMBT-2pqwA03A:453-520

(-) 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 2rhi 2rhu 2rhx 2rhy 2rhz 2ri2 2ri3 2ri5 2rjc 2rjd 2rje 2rjf 3oq5 3p8h 3uwn

(-) Related Entries Specified in the PDB File

2rjc CRYSTAL STRUCTURE OF L3MBTL1 PROTEIN IN COMPLEX WITH MES
2rjd CRYSTAL STRUCTURE OF L3MBTL1 PROTEIN
2rje CRYSTAL STRUCTURE OF L3MBTL1 IN COMPLEX WITH H4K20ME2 (RESIDUES 17-25), ORTHORHOMBIC FORM II
2rjf CRYSTAL STRUCTURE OF L3MBTL1 IN COMPLEX WITH H4K20ME2 (RESIDUES 12-30), ORTHORHOMBIC FORM I