Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Biol.Unit 1 - manually
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Biol.Unit 1 - manually
Biol.Unit 1 - manually  (Jmol Viewer)
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  STRUCTURAL BASIS OF SEQUENCE-SPECIFIC RECRUITMENT OF HISTONE DEACETYLASES BY MYOCYTE ENHANCER FACTOR-2
 
Authors :  A. Han, F. Pan, J. C. Stroud, H. D. Youn, J. O. Liu, L. Chen
Date :  11 Nov 02  (Deposition) - 11 Nov 03  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,G  (2x)
Biol. Unit 1:  A,B,C,D,G  (1x)
Keywords :  Mads-Box, Protein-Dna Complex, Histone Deacetylases, Transcription- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Han, F. Pan, J. C. Stroud, H. D. Youn, J. O. Liu, L. Chen
Sequence-Specific Recruitment Of Transcriptional Co-Repressor Cabin1 By Myocyte Enhancer Factor-2
Nature V. 422 730 2003
PubMed-ID: 12700764  |  Reference-DOI: 10.1038/NATURE01555

(-) Compounds

Molecule 1 - 5'-D(*AP*GP*CP*TP*AP*TP*TP*TP*AP*TP*AP*AP*GP*C)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*GP*CP*TP*TP*AP*TP*AP*AP*AP*TP*AP*GP*CP*T)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - MYOCYTE-SPECIFIC ENHANCER FACTOR 2B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 2-91, MADS-BOX/MEF2S DOMAIN
    Gene: MEF2B OR XMEF2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SERUM RESPONSE FACTOR-LIKE PROTEIN 2, XMEF2, RSRFR2
 
Molecule 4 - CALCINEURIN-BINDING PROTEIN CABIN 1
    Chains: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 101-132, CABIN1, MEF2-BINDING DOMAIN
    Gene: CABIN1 OR KIAA0330
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CALCINEURIN INHIBITOR, CHAIN

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit (2x): ABCDG
Biological Unit 1 (1x): ABCDG

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1N6J)

(-) Sites  (0, 0)

(no "Site" information available for 1N6J)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N6J)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1N6J)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N6J)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MADS_BOX_1PS00350 MADS-box domain signature.MEF2B_HUMAN3-57
 		  2A:3-57
B:3-57
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MADS_BOX_1PS00350 MADS-box domain signature.MEF2B_HUMAN3-57
 		  2A:3-57
B:3-57

(-) Exons   (2, 2)

Asymmetric Unit (2, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003983192bENSE00001631216chr22:24407868-24408178311CABIN_HUMAN-00--
1.3ENST000003983193ENSE00001361081chr22:24431892-2443196877CABIN_HUMAN1-110--
1.4ENST000003983194ENSE00001257233chr22:24432537-2443262993CABIN_HUMAN2-32310--
1.5ENST000003983195ENSE00000651602chr22:24434796-24434909114CABIN_HUMAN33-70380--
1.6ENST000003983196ENSE00000651603chr22:24437587-24437721135CABIN_HUMAN71-115450--
1.7ENST000003983197ENSE00000651604chr22:24439366-24439546181CABIN_HUMAN116-176610--
1.8ENST000003983198ENSE00000651605chr22:24445553-24445682130CABIN_HUMAN176-219440--
1.9ENST000003983199ENSE00000651606chr22:24447287-24447436150CABIN_HUMAN219-269510--
1.10aENST0000039831910aENSE00000651607chr22:24451336-24451622287CABIN_HUMAN269-365970--
1.11cENST0000039831911cENSE00000651608chr22:24452655-24452823169CABIN_HUMAN365-421570--
1.12ENST0000039831912ENSE00000651609chr22:24455690-24455826137CABIN_HUMAN421-467470--
1.13ENST0000039831913ENSE00000651610chr22:24456387-24456604218CABIN_HUMAN467-539730--
1.14ENST0000039831914ENSE00000651611chr22:24458410-2445848879CABIN_HUMAN540-566270--
1.15ENST0000039831915ENSE00000651612chr22:24459422-24459609188CABIN_HUMAN566-628630--
1.16ENST0000039831916ENSE00000651613chr22:24460498-24460650153CABIN_HUMAN629-679510--
1.17aENST0000039831917aENSE00001256688chr22:24462938-24463132195CABIN_HUMAN680-744650--
1.18aENST0000039831918aENSE00000651615chr22:24466751-24466993243CABIN_HUMAN745-825810--
1.19ENST0000039831919ENSE00000651616chr22:24468304-24468460157CABIN_HUMAN826-878530--
1.20ENST0000039831920ENSE00000651617chr22:24472118-24472233116CABIN_HUMAN878-916390--
1.21ENST0000039831921ENSE00000651618chr22:24479181-24479342162CABIN_HUMAN917-970540--
1.22ENST0000039831922ENSE00000651619chr22:24480532-24480738207CABIN_HUMAN971-1039690--
1.23ENST0000039831923ENSE00000651620chr22:24480959-24481104146CABIN_HUMAN1040-1088490--
1.24aENST0000039831924aENSE00000651622chr22:24483405-24483666262CABIN_HUMAN1088-1175880--
1.25aENST0000039831925aENSE00000651625chr22:24487537-24487797261CABIN_HUMAN1176-1262870--
1.26ENST0000039831926ENSE00000651626chr22:24491894-24492045152CABIN_HUMAN1263-1313510--
1.27bENST0000039831927bENSE00000651628chr22:24493977-24494155179CABIN_HUMAN1313-1373610--
1.28ENST0000039831928ENSE00000651629chr22:24509533-24509715183CABIN_HUMAN1373-1434620--
1.29bENST0000039831929bENSE00000651631chr22:24515334-24515665332CABIN_HUMAN1434-15441110--
1.30ENST0000039831930ENSE00000651632chr22:24530269-24530382114CABIN_HUMAN1545-1582380--
1.35bENST0000039831935bENSE00000651635chr22:24560368-24560531164CABIN_HUMAN1583-1637550--
1.36ENST0000039831936ENSE00000879517chr22:24561498-2456159497CABIN_HUMAN1637-1669330--
1.37aENST0000039831937aENSE00000879518chr22:24562607-24563281675CABIN_HUMAN1670-18942250--
1.38ENST0000039831938ENSE00000879519chr22:24564415-2456448975CABIN_HUMAN1895-1919250--
1.39ENST0000039831939ENSE00000651645chr22:24567681-24567963283CABIN_HUMAN1920-2014950--
1.41bENST0000039831941bENSE00000651649chr22:24572079-24572243165CABIN_HUMAN2014-2069560--
1.42bENST0000039831942bENSE00001256752chr22:24573472-24573785314CABIN_HUMAN2069-21731051G:101-11515
1.43bENST0000039831943bENSE00001257253chr22:24574021-24574596576CABIN_HUMAN2174-2220471G:116-12611

(-) Sequences/Alignments

Asymmetric 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:93
 aligned with MEF2B_HUMAN | Q02080 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:93
                                    11        21        31        41        51        61        71        81        91   
         MEF2B_HUMAN      2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRRGIG   94
               SCOP domains d1n6ja_ A: Myocyte enhancer factor Mef2b core                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeee..hhhhhhhhhhh.....eeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: A:3-57 UniProt: 3-57                  ------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------- Transcript
                1n6j A    2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRRGIG   94
                                    11        21        31        41        51        61        71        81        91   


Chain B from PDB  Type:PROTEIN  Length:90
 aligned with MEF2B_HUMAN | Q02080 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:90
                                    11        21        31        41        51        61        71        81        91
         MEF2B_HUMAN      2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR   91
               SCOP domains d1n6jb_ B: Myocyte enhancer factor Mef2b core                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------SRF-TF-1n6jB01 B:9-59                              -------------------------------- Pfam domains (1)
           Pfam domains (2) -------SRF-TF-1n6jB02 B:9-59                              -------------------------------- Pfam domains (2)
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeee..hhhhhhhhhhh.....eeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: B:3-57 UniProt: 3-57                  ---------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                1n6j B    2 GRKKIQISRILDQRNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSANRLFQYASTDMDRVLLKYTEYSEPHESRTNTDILETLKRR   91
                                    11        21        31        41        51        61        71        81        91


Chain C from PDB  Type:DNA  Length:14
                                               
                1n6j C    3 AGCTATTTATAAGC   16
                                    12    


Chain D from PDB  Type:DNA  Length:14
                                               
                1n6j D    3 GCTTATAAATAGCT   16
                                    12    


Chain G from PDB  Type:PROTEIN  Length:26
 aligned with CABIN_HUMAN | Q9Y6J0 from UniProtKB/Swiss-Prot  Length:2220

    Alignment length:26
                                  2168      2178      
         CABIN_HUMAN   2159 SPKGSISEETKQKLKSAILSAQSAAN 2184
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains MEF2_binding-1n6jG01       Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
               Transcript 1 Exon 1.42b     Exon 1.43b  Transcript 1
                1n6j G  101 SPKGSISEETKQKLKSAILSAQSAAN  126
                                   110       120
   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, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1N6J)

(-) Pfam Domains  (2, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: MEF2_binding] (1)
(-)
Clan: no clan defined [family: SRF-TF] (4)

(-) Gene Ontology  (25, 26)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MEF2B_HUMAN | Q02080)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    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:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
biological process
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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: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:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

Chain G   (CABIN_HUMAN | Q9Y6J0)
molecular function
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0030346    protein phosphatase 2B binding    Interacting selectively and non-covalently with the enzyme protein phosphatase 2B.
    GO:0004864    protein phosphatase inhibitor activity    Stops, prevents or reduces the activity of a protein phosphatase, an enzyme that hydrolyzes phosphate groups from phosphorylated proteins.
biological process
    GO:0006336    DNA replication-independent nucleosome assembly    The formation of nucleosomes outside the context of DNA replication.
    GO:0007166    cell surface receptor signaling pathway    A series of molecular signals initiated by activation of a receptor on the surface of a cell. The pathway begins with binding of an extracellular ligand to a cell surface receptor, or for receptors that signal in the absence of a ligand, by ligand-withdrawal or the activity of a constitutively active receptor. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0043086    negative regulation of catalytic activity    Any process that stops or reduces the activity of an enzyme.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0014823    response to activity    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 activity stimulus.
cellular component
    GO:0016235    aggresome    An inclusion body formed by dynein-dependent retrograde transport of an aggregated protein on microtubules.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  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
(no "Ligands, Modified Residues, Ions" information available for 1n6j)
 
  Sites
(no "Sites" information available for 1n6j)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1n6j)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 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
  1n6j
    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
  CABIN_HUMAN | Q9Y6J0
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  MEF2B_HUMAN | Q02080
    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
  CABIN_HUMAN | Q9Y6J0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  MEF2B_HUMAN | Q02080
    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
        MEF2B_HUMAN | Q02080: 1tqe

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1N6J)