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(-) Description

Title :  CRYSTAL STRUCTURE OF MEF2A CORE BOUND TO DNA
 
Authors :  E. Santelli, T. J. Richmond
Date :  17 Feb 00  (Deposition) - 20 Mar 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,E,F  (1x)
Biol. Unit 2:  C,D,G,H  (1x)
Keywords :  Mads-Box Transcription Factor, Dna/Protein Complex, Transcription/Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Santelli, T. J. Richmond
Crystal Structure Of Mef2A Core Bound To Dna At 1. 5 A Resolution.
J. Mol. Biol. V. 297 437 2000
PubMed-ID: 10715212  |  Reference-DOI: 10.1006/JMBI.2000.3568
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3')
    Chains: E, H
    Engineered: YES
    Other Details: CONSENSUS DNA BINDING SITE FOR MEF2
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3')
    Chains: F, G
    Engineered: YES
    Other Details: CONSENSUS DNA BINDING SITE FOR MEF2
    Synthetic: YES
 
Molecule 3 - MADS BOX TRANSCRIPTION ENHANCER FACTOR 2, POLYPEPTIDE A
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: N-TERMINUS, RESIDUES 2-78
    Organ: HEART, SKELETAL MUSCLE
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MEF2A TRANSCRIPTION FACTOR, MYOCYTE ENHANCER FACTOR 2A, MYOCYTE-SPECIFIC ENHANCER FACTOR 2A, SERUM RESPONSE FACTOR-LIKE PROTEIN 1

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB  EF  
Biological Unit 2 (1x):   CD  GH

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 1EGW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MADS_BOX_1PS00350 MADS-box domain signature.MEF2A_HUMAN3-57
 
 
 		  4A:3-57
B:3-57
C:3-57
D:3-57
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MADS_BOX_1PS00350 MADS-box domain signature.MEF2A_HUMAN3-57
 
 
 		  2A:3-57
B:3-57
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MADS_BOX_1PS00350 MADS-box domain signature.MEF2A_HUMAN3-57
 
 
 		  2-
-
C:3-57
D:3-57

(-) Exons   (0, 0)

(no "Exon" information available for 1EGW)

(-) 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:71
 aligned with MEF2A_HUMAN | Q02078 from UniProtKB/Swiss-Prot  Length:507

    Alignment length:71
                                    11        21        31        41        51        61        71 
           MEF2A_HUMAN    2 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY 72
               SCOP domains d1egwa_ A: Myocyte enhancer factor Mef2a core                           SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeee..hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: A:3-57 UniProt: 3-57                  --------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1egw A  2 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY 72
                                    11        21        31        41        51        61        71 


Chain B from PDB  Type:PROTEIN  Length:72
 aligned with MEF2A_HUMAN | Q02078 from UniProtKB/Swiss-Prot  Length:507

    Alignment length:72
                                    11        21        31        41        51        61        71  
           MEF2A_HUMAN    2 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEYN 73
               SCOP domains d1egwb_ B: Myocyte enhancer factor Mef2a core                            SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: B:3-57 UniProt: 3-57                  ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  1egw B  2 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEYN 73
                                    11        21        31        41        51        61        71  


Chain C from PDB  Type:PROTEIN  Length:72
 aligned with MEF2A_HUMAN | Q02078 from UniProtKB/Swiss-Prot  Length:507

    Alignment length:72
                                    11        21        31        41        51        61        71  
           MEF2A_HUMAN    2 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEYN 73
               SCOP domains d1egwc_ C: Myocyte enhancer factor Mef2a core                            SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.....eeeee..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: C:3-57 UniProt: 3-57                  ---------------- PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                  1egw C  2 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEYN 73
                                    11        21        31        41        51        61        71  


Chain D from PDB  Type:PROTEIN  Length:71
 aligned with MEF2A_HUMAN | Q02078 from UniProtKB/Swiss-Prot  Length:507

    Alignment length:71
                                    11        21        31        41        51        61        71 
           MEF2A_HUMAN    2 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY 72
               SCOP domains d1egwd_ D: Myocyte enhancer factor Mef2a core                           SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeee..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -MADS_BOX_1  PDB: D:3-57 UniProt: 3-57                  --------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                  1egw D  2 GRKKIQITRIMDERNRQVTFTKRKFGLMKKAYELSVLCDCEIALIIFNSSNKLFQYASTDMDKVLLKYTEY 72
                                    11        21        31        41        51        61        71 


Chain E from PDB  Type:DNA  Length:17
                                                
                  1egw E  1 AAAGCTATTATTAGCTT 17
                                    10       


Chain F from PDB  Type:DNA  Length:17
                                                
                  1egw F  1 TAAGCTAATAATAGCTT 17
                                    10       


Chain G from PDB  Type:DNA  Length:17
                                                
                  1egw G  1 TAAGCTAATAATAGCTT 17
                                    10       


Chain H from PDB  Type:DNA  Length:17
                                                
                  1egw H  1 AAAGCTATTATTAGCTT 17
                                    10
   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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (45, 45)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MEF2A_HUMAN | Q02078)
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:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0001105    RNA polymerase II transcription coactivator activity    Interacting selectively and non-covalently with an RNA polymerase II (RNAP II) regulatory transcription factor and also with the RNAP II basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between activating transcription factors and the basal RNAP II transcription machinery.
    GO:0000981    RNA polymerase II transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription by RNA polymerase II. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    GO:0046332    SMAD binding    Interacting selectively and non-covalently with a SMAD signaling protein.
    GO:0033613    activating transcription factor binding    Interacting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription.
    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:0035035    histone acetyltransferase binding    Interacting selectively and non-covalently with the enzyme histone acetyltransferase.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    GO:0003705    transcription factor activity, RNA polymerase II distal enhancer sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in a distal enhancer region for RNA polymerase II (RNAP II) in order to modulate transcription by RNAP II.
    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:0070375    ERK5 cascade    An intracellular protein kinase cascade containing at least ERK5 (also called BMK1; a MAPK), a MEK (a MAPKK) and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0061337    cardiac conduction    Transfer of an organized electrical impulse across the heart to coordinate the contraction of cardiac muscles. The process begins with generation of an action potential (in the sinoatrial node (SA) in humans) and ends with a change in the rate, frequency, or extent of the contraction of the heart muscles.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0071277    cellular response to calcium ion    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 calcium ion stimulus.
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    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:0000002    mitochondrial genome maintenance    The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.
    GO:0048311    mitochondrion distribution    Any process that establishes the spatial arrangement of mitochondria between and within cells.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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: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:0007399    nervous system development    The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
    GO:0051149    positive regulation of muscle cell differentiation    Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
    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: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: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.
    GO:0055005    ventricular cardiac myofibril assembly    The process whose specific outcome is the progression of the ventricular cardiac myofibril over time, from its formation to the mature structure. A cardiac myofibril is a myofibril specific to cardiac muscle cells.
cellular component
    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: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: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.

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        MEF2A_HUMAN | Q02078: 1c7u 1lew 3kov 3mu6 3p57

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