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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST MBT DOMAIN FROM HUMAN KIAA1798 PROTEIN
 
Authors :  T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  29 May 04  (Deposition) - 29 Nov 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Mbt Domain, Kiaa1798, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Tomizawa, T. Kigawa, S. Koshiba, M. Inoue, S. Yokoyama
Solution Structure Of The First Mbt Domain From Human Kiaa1798 Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - KIAA1798 PROTEIN
    Chains: A
    Engineered: YES
    Expression System Plasmid: P040119-27
    Expression System Vector Type: PLASMID
    Fragment: MBT DOMAIN
    Gene: KAZUSA CDNA FJ20547
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CELL-FREE PROTEIN SYNTHESIS

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1WJS)

(-) Sites  (0, 0)

(no "Site" information available for 1WJS)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1WJS)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1WJS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1WJS)

(-) PROSITE Motifs  (1, 2)

NMR Structure (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MBTPS51079 MBT repeat profile.LMBL3_HUMAN232-332
340-439
448-543		  2A:8-82
A:90-127
-

(-) Exons   (6, 6)

NMR Structure (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.5cENST000003681365cENSE00002182355chr6:130341702-130341813112LMBL3_HUMAN-00--
1.6ENST000003681366ENSE00001409294chr6:130343372-13034345079LMBL3_HUMAN-00--
1.7ENST000003681367ENSE00001411632chr6:130363830-130363946117LMBL3_HUMAN1-34340--
1.8ENST000003681368ENSE00000975595chr6:130370427-130370538112LMBL3_HUMAN35-72380--
1.9bENST000003681369bENSE00001084666chr6:130370901-13037097575LMBL3_HUMAN72-97260--
1.10bENST0000036813610bENSE00000975596chr6:130372394-130372553160LMBL3_HUMAN97-150540--
1.11bENST0000036813611bENSE00000975597chr6:130374004-130374136133LMBL3_HUMAN150-194450--
1.12bENST0000036813612bENSE00000975598chr6:130376316-13037640085LMBL3_HUMAN195-223291A:1-7 (gaps)19
1.13ENST0000036813613ENSE00002162936chr6:130378551-13037864292LMBL3_HUMAN223-253310--
1.14ENST0000036813614ENSE00002186523chr6:130381181-130381285105LMBL3_HUMAN254-288351A:8-3831
1.15ENST0000036813615ENSE00002186040chr6:130387498-130387633136LMBL3_HUMAN289-334461A:39-8446
1.16bENST0000036813616bENSE00000975602chr6:130389475-13038956692LMBL3_HUMAN334-364311A:84-11431
1.17bENST0000036813617bENSE00000975603chr6:130392121-130392272152LMBL3_HUMAN365-415511A:115-124 (gaps)21
1.18ENST0000036813618ENSE00002154851chr6:130399703-13039977977LMBL3_HUMAN415-441271A:125-127 (gaps)9
1.19ENST0000036813619ENSE00002160966chr6:130404765-13040485086LMBL3_HUMAN441-469290--
1.20ENST0000036813620ENSE00002177917chr6:130407285-130407395111LMBL3_HUMAN470-506370--
1.21bENST0000036813621bENSE00000975607chr6:130413890-130414004115LMBL3_HUMAN507-545390--
1.22ENST0000036813622ENSE00000975608chr6:130415410-130415512103LMBL3_HUMAN545-579350--
1.23ENST0000036813623ENSE00000975609chr6:130425571-130425720150LMBL3_HUMAN579-629510--
1.24ENST0000036813624ENSE00000975610chr6:130442024-13044210380LMBL3_HUMAN629-656280--
1.25ENST0000036813625ENSE00000975611chr6:130454597-130454766170LMBL3_HUMAN656-712570--
1.26ENST0000036813626ENSE00000975612chr6:130454988-13045505063LMBL3_HUMAN713-733210--
1.27dENST0000036813627dENSE00002176826chr6:130460755-1304625841830LMBL3_HUMAN734-780470--

(-) 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:127
 aligned with LMBL3_HUMAN | Q96JM7 from UniProtKB/Swiss-Prot  Length:780

    Alignment length:223
                                   214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424   
          LMBL3_HUMAN   205 GSQRARRKRRGDSAVLKQGLPPKGKKAWCWASYLEEEKAVAVPAKLFKEHQSFPYNKNGFKVGMKLEGVDPEHQSVYCVLTVAEVCGYRIKLHFDGYSDCYDFWVNADALDIHPVGWCEKTGHKLHPPKGYKEEEFNWQTYLKTCKAQAAPKSLFENQNITVIPSGFRVGMKLEAVDKKNPSFICVATVTDMVDNRFLVHFDNWDESYDYWCEASSPHIHPVG 427
               SCOP domains d1w       jsa     _                                   A: Lethal(3)malignant brain tumor-like 3 protein, L3MBTL3 (KIAA1798)                                                                                                      SCOP domains
               CATH domains 1wj       sA0     0                                   A:1-127  [code=2.30.30.160, no name defined]                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------MBT-1wjsA01 A:18-90                                                      --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...-------...-----.----------------------------------...........eeeeee..eeeeeeeeeeeeee..eeeeee...hhhhheeee..........hhhhhh..............hhhhhhhhh.....hhhhhh...........-----------...---------------------------------..------. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------MBT  PDB: A:8-82 UniProt: 232-332                                                                    -------MBT  PDB: A:90-127 UniProt: 340-439                                                      PROSITE
           Transcript 1 (1) Exon 1.12b         ------------------------------Exon 1.14  PDB: A:8-38 [INCOMPLETE]Exon 1.15  PDB: A:39-84 UniProt: 289-334      ------------------------------Exon 1.17b  PDB: A:115-124 (gaps) UniProt: 365-415 ------------ Transcript 1 (1)
           Transcript 1 (2) ------------------Exon 1.13  PDB: -              --------------------------------------------------------------------------------Exon 1.16b  PDB: A:84-114      --------------------------------------------------Exon 1.18     Transcript 1 (2)
                 1wjs A   1 GSS-------GSS-----G----------------------------------PYNKNGFKVGMKLEGVDPEHQSVYCVLTVAEVCGYRIKLHFDGYSDCYDFWVNADALDIHPVGWCEKTGHKLHPPKGYKEEEFNWQTYLKTCKAQAAPKSLFENQNITVIPSGF-----------SGP---------------------------------SS------G 127
                              |      -| |     |-         -         -         -   |    14        24        34        44        54        64        74        84        94       104       114      |  -       123|        -         -         -    ||   -  |
                              3       4 6     7                                  8                                                                                                              121         122 |                               125|    127
                                                                                                                                                                                                              124                                126
   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  (1, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: Tudor (88)

(-) Gene Ontology  (9, 9)

NMR Structure(hide GO term definitions)
Chain A   (LMBL3_HUMAN | Q96JM7)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
    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).
biological process
    GO:0043249    erythrocyte maturation    A developmental process, independent of morphogenetic (shape) change, that is required for an erythrocyte to attain its fully functional state.
    GO:0030851    granulocyte differentiation    The process in which a myeloid precursor cell acquires the specialized features of a granulocyte. Granulocytes are a class of leukocytes characterized by the presence of granules in their cytoplasm. These cells are active in allergic immune reactions such as arthritic inflammation and rashes. This class includes basophils, eosinophils and neutrophils.
    GO:0030225    macrophage differentiation    The process in which a relatively unspecialized monocyte acquires the specialized features of a macrophage.
    GO:0030099    myeloid cell differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte, megakaryocyte, thrombocyte, or erythrocyte lineages.
    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: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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        LMBL3_HUMAN | Q96JM7: 1wjq 3ut1 4fl6 4l59

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