Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - model 1, sites
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - model 1, sites
NMR Structure - model 1, sites  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION NMR STRUCTURE OF THE PHD DOMAIN OF HUMAN MLL5, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR6512A
 
Authors :  A. Lemak, A. Yee, S. Houliston, M. Garcia, H. Wu, J. Min, G. T. Montelione C. Arrowsmith, Northeast Structural Genomics Consortium (Nesg Structural Genomics Consortium (Sgc), Chaperone-Enabled Stud Epigenetic Regulation Enzymes (Cebs)
Date :  29 Jun 12  (Deposition) - 05 Sep 12  (Release) - 28 Nov 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Zinc Finger, Transcription, Protein Binding, Nesg, Northeast Structural Genomics Consortium, Sgc, Structural Genomics Consortium, Psi-Biology, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Lemak, A. Yee, S. Houliston, M. Garcia, H. Wu, J. Min, G. T. Montelione, C. Arrowsmith
Nmr Solution Structure Of The Human Mll5 Phd Domain (Casp Target)
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE MLL5
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System VectorPET28B
    FragmentPHD-TYPE DOMAIN RESIDUES 109-188
    GeneMLL5, KMT2E
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLYSINE N-METHYLTRANSFERASE 2E, KMT2E, MYELOID/LYMPHOID OR MIXED-LINEAGE LEUKEMIA PROTEIN 5

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION
NMR Structure * (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:121 , CYS A:123 , HIS A:143 , CYS A:146 , GLN A:177BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:135 , CYS A:138 , CYS A:160 , CYS A:163BINDING SITE FOR RESIDUE ZN A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2LV9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2LV9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2LV9)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.KMT2E_HUMAN118-166  1A:118-166
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.KMT2E_HUMAN121-163  1A:121-163
NMR Structure * (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_PHD_2PS50016 Zinc finger PHD-type profile.KMT2E_HUMAN118-166  1A:118-166
2ZF_PHD_1PS01359 Zinc finger PHD-type signature.KMT2E_HUMAN121-163  1A:121-163

(-) Exons   (0, 0)

(no "Exon" information available for 2LV9)

(-) Sequences/Alignments

NMR Structure
   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:80
 aligned with KMT2E_HUMAN | Q8IZD2 from UniProtKB/Swiss-Prot  Length:1858

    Alignment length:80
                                   118       128       138       148       158       168       178       188
          KMT2E_HUMAN   109 SEDGSYGTDVTRCICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPRNLDKERAVLLQRRKRENMSDGD 188
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......................eee......eee.........................hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------ZF_PHD_2  PDB: A:118-166 UniProt: 118-166        ---------------------- PROSITE (1)
                PROSITE (2) ------------ZF_PHD_1  PDB: A:121-163 UniProt: 121-163  ------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------- Transcript
                 2lv9 A 109 SEDGSYGTDVTRCICGFTHDDGYMICCDKCSVWQHIDCMGIDRQHIPDTYLCERCQPRNLDKERAVLLQRRKRENMSDGD 188
                                   118       128       138       148       158       168       178       188

   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 2LV9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2LV9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2LV9)

(-) Gene Ontology  (32, 32)

NMR Structure(hide GO term definitions)
Chain A   (KMT2E_HUMAN | Q8IZD2)
molecular function
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0042800    histone methyltransferase activity (H3-K4 specific)    Catalysis of the reaction: S-adenosyl-L-methionine + histone H3 L-lysine (position 4) = S-adenosyl-L-homocysteine + histone H3 N6-methyl-L-lysine (position 4). This reaction is the addition of a methyl group onto lysine at position 4 of the histone H3 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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating 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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006306    DNA methylation    The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    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:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0071300    cellular response to retinoic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0030218    erythrocyte differentiation    The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
    GO:0051568    histone H3-K4 methylation    The modification of histone H3 by addition of one or more methyl groups to lysine at position 4 of the histone.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0042119    neutrophil activation    The change in morphology and behavior of a neutrophil resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0002446    neutrophil mediated immunity    Any process involved in the carrying out of an immune response by a neutrophil.
    GO:0030854    positive regulation of granulocyte differentiation    Any process that activates or increases the frequency, rate or extent of granulocyte differentiation.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048384    retinoic acid receptor signaling pathway    The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0070688    MLL5-L complex    A protein complex that can methylate lysine-4 of histone H3 and plays an essential role in retinoic-acid-induced granulopoiesis. MLL5 is the catalytic methyltransferase subunit, and the complex also contains serine/threonine kinase 38 (STK38), protein phosphatase 1 catalytic subunits, the host cell factor-1 N-terminal subunit, beta-actin, and O-GlcNAc transferase; the human genes encoding the subunits are MLL5, STK38, PPP1CA, PPP1CB, PPP1CC, HCFC1, ACTB and OGT, respectively.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0045171    intercellular bridge    A direct connection between the cytoplasm of two cells that is formed following the completion of cleavage furrow ingression during cell division. They are usually present only briefly prior to completion of cytokinesis. However, in some cases, such as the bridges between germ cells during their development, they become stabilised.
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0016607    nuclear speck    A discrete extra-nucleolar subnuclear domain, 20-50 in number, in which splicing factors are seen to be localized by immunofluorescence microscopy.
    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.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2lv9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2lv9
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  KMT2E_HUMAN | Q8IZD2
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.43
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  KMT2E_HUMAN | Q8IZD2
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        KMT2E_HUMAN | Q8IZD24l58 5ht6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2LV9)