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 - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE METHYL-CPG-BINDING DOMAIN OF HUMAN MBD1 IN COMPLEX WITH METHYLATED DNA
 
Authors :  I. Ohki, N. Shimotake, N. Fujita, J. -G. Jee, T. Ikegami, M. Nakao, M. Shirakawa
Date :  17 Apr 01  (Deposition) - 30 May 01  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B,C  (20x)
Keywords :  Protein-Dna Complex, Alpha-Beta, Double Helix, Recognition Via Beta-Sheet, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Ohki, N. Shimotake, N. Fujita, J. Jee, T. Ikegami, M. Nakao, M. Shirakawa
Solution Structure Of The Methyl-Cpg Binding Domain Of Human Mbd1 In Complex With Methylated Dna.
Cell(Cambridge, Mass. ) V. 105 487 2001
PubMed-ID: 11371345  |  Reference-DOI: 10.1016/S0092-8674(01)00324-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHYL-CPG BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-2T
    Expression System Strain: DH5A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: METHYL-CPG-BINDING DOMAIN
    Gene: MBD1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - 5'-D(*GP*TP*AP*TP*CP*(5CM)P*GP*GP*AP*TP*AP*C)-3'
    Chains: B, C
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

NMR Structure (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 1IG4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1IG4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IG4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IG4)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MBDPS50982 Methyl-CpG-binding domain (MBD) profile.MBD1_HUMAN1-69  1A:1-69

(-) Exons   (2, 2)

NMR Structure (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003829481aENSE00001211676chr18:47808144-47807733412MBD1_HUMAN-00--
1.3aENST000003829483aENSE00001682699chr18:47806387-47806253135MBD1_HUMAN1-37371A:1-3737
1.4ENST000003829484ENSE00000950204chr18:47803574-47803460115MBD1_HUMAN37-75391A:37-7539
1.5ENST000003829485ENSE00000950205chr18:47803368-47803202167MBD1_HUMAN76-131560--
1.6ENST000003829486ENSE00000950206chr18:47803114-4780303283MBD1_HUMAN131-159290--
1.7ENST000003829487ENSE00000950207chr18:47802788-4780274841MBD1_HUMAN159-172140--
1.8ENST000003829488ENSE00000950219chr18:47802351-47802205147MBD1_HUMAN173-221490--
1.9ENST000003829489ENSE00000950208chr18:47802098-47801970129MBD1_HUMAN222-264430--
1.11ENST0000038294811ENSE00000950209chr18:47801615-47801499117MBD1_HUMAN265-303390--
1.12ENST0000038294812ENSE00000950210chr18:47801415-4780134769MBD1_HUMAN304-326230--
1.14ENST0000038294814ENSE00000950212chr18:47800233-47799934300MBD1_HUMAN327-4261000--
1.16bENST0000038294816bENSE00000950214chr18:47799325-47799194132MBD1_HUMAN427-470440--
1.17ENST0000038294817ENSE00001640699chr18:47799108-4779904762MBD1_HUMAN471-491210--
1.20cENST0000038294820cENSE00001724709chr18:47796181-47796046136MBD1_HUMAN491-535450--

(-) 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:75
 aligned with MBD1_HUMAN | Q9UIS9 from UniProtKB/Swiss-Prot  Length:605

    Alignment length:75
                                    10        20        30        40        50        60        70     
           MBD1_HUMAN     1 MAEDWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLTLFDFKQGILCYPAPK  75
               SCOP domains d1ig4a_ A: Methylation-dependent transcriptional repressor MBD1/PCM1        SCOP domains
               CATH domains 1ig4A00 A:1-75 Methyl-cpg-binding Protein 2; Chain A                        CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee........eeeee...........eeeee.....ee.hhhhhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE MBD  PDB: A:1-69 UniProt: 1-69                                       ------ PROSITE
           Transcript 1 (1) Exon 1.3a  PDB: A:1-37 UniProt: 1-37 -------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------Exon 1.4  PDB: A:37-75 UniProt: 37-75   Transcript 1 (2)
                 1ig4 A   1 MAEDWLDCPALGPGWKRREVFRKSGATCGRSDTYYQSPTGDRIRSKVELTRYLGPACDLTLFDFKQGILCYPAPK  75
                                    10        20        30        40        50        60        70     


Chain B from PDB  Type:DNA  Length:12
                                            
                 1ig4 B 101 GTATCcGGATAC 112
                                 | 110  
                               106-5CM  


Chain C from PDB  Type:DNA  Length:12
                                            
                 1ig4 C 113 GTATCcGGATAC 124
                                 | 122  
                               118-5CM
   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: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1IG4)

(-) Gene Ontology  (30, 30)

NMR Structure(hide GO term definitions)
Chain A   (MBD1_HUMAN | Q9UIS9)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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:0010385    double-stranded methylated DNA binding    Interacting selectively and non-covalently with double-stranded methylated DNA. Methylation of cytosine or adenine in DNA is an important mechanism for establishing stable heritable epigenetic marks.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008327    methyl-CpG binding    Interacting selectively and non-covalently with a methylated cytosine/guanine dinucleotide.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0006346    methylation-dependent chromatin silencing    Repression of transcription by methylation of DNA, leading to the formation of heterochromatin.
    GO:0048712    negative regulation of astrocyte differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of astrocyte differentiation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    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:0030182    neuron differentiation    The process in which a relatively unspecialized cell acquires specialized features of a neuron.
    GO:0044030    regulation of DNA methylation    Any process that modulates the frequency, rate or extent of the covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0042220    response to cocaine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cocaine stimulus. Cocaine is a crystalline alkaloid obtained from the leaves of the coca plant.
    GO:0032355    response to estradiol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0014076    response to fluoxetine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fluoxetine stimulus. Fluoxetine increases the extracellular level of the neurotransmitter serotonin by inhibiting its reuptake into the presynaptic cell, increasing the level of serotonin available to bind to the postsynaptic receptor.
    GO:0031667    response to nutrient levels    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus reflecting the presence, absence, or concentration of nutrients.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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: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.

 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
    5CM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1ig4)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ig4)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1ig4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MBD1_HUMAN | Q9UIS9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MBD1_HUMAN | Q9UIS9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MBD1_HUMAN | Q9UIS9: 1d9n 4d4w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1IG4)