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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HOMEOBOX DOMAIN OF HUMAN HOMEOBOX PROTEIN MEIS2
 
Authors :  R. Lam, M. Soloveychik, K. P. Battaile, V. Romanov, K. Lam, I. Beletskay E. Gordon, E. F. Pai, N. Y. Chirgadze
Date :  29 Sep 09  (Deposition) - 13 Oct 10  (Release) - 13 Oct 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (8x)
Keywords :  Homeobox Domain, Human Homeobox Protein Meis2, Dna-Binding, Transcription, Homeobox, Nucleus, Phosphoprotein, Dna Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. Lam, M. Soloveychik, K. P. Battaile, V. Romanov, K. Lam, I. Beletskaya, E. Gordon, E. F. Pai, N. Y. Chirgadze
Crystal Structure Of The Homeobox Domain Of Human Homeobox Protein Meis2
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HOMEOBOX PROTEIN MEIS2
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28-LIC
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 281-345 (HOMEOBOX DOMAIN)
    GeneMEIS2, MRG1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMEIS1-RELATED PROTEIN 1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (8x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CL2Ligand/IonCHLORIDE ION
3MSE4Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (2, 48)
No.NameCountTypeFull Name
1ACT16Ligand/IonACETATE ION
2CL-1Ligand/IonCHLORIDE ION
3MSE32Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:4 , ARG A:292BINDING SITE FOR RESIDUE CL A 500
2AC2SOFTWAREGLN A:297 , LEU A:299 , ARG B:331BINDING SITE FOR RESIDUE ACT A 510
3AC3SOFTWAREHOH B:1 , ARG B:292BINDING SITE FOR RESIDUE CL B 500
4AC4SOFTWAREARG A:331 , GLN B:297 , LEU B:299BINDING SITE FOR RESIDUE ACT B 510

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3K2A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3K2A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3K2A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3K2A)

(-) Exons   (0, 0)

(no "Exon" information available for 3K2A)

(-) 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:55
 aligned with MEIS2_HUMAN | O14770 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:55
                                   293       303       313       323       333     
          MEIS2_HUMAN   284 PKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPM 338
               SCOP domains d3k2aa_ A: automated matches                            SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                 3k2a A 284 PKVATNImRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPm 338
                                   293       303       313       323       333    |
                                 291-MSE                                        338-MSE

Chain B from PDB  Type:PROTEIN  Length:56
 aligned with MEIS2_HUMAN | O14770 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:56
                                   292       302       312       322       332      
          MEIS2_HUMAN   283 FPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPM 338
               SCOP domains d3k2ab_ B: automated matches                             SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
           Pfam domains (1) -----------Homeobox_KN-3k2aB01 B:294-333           ----- Pfam domains (1)
           Pfam domains (2) -----------Homeobox_KN-3k2aB02 B:294-333           ----- Pfam domains (2)
         Sec.struct. author .hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 3k2a B 283 FPKVATNImRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPm 338
                                   292       302       312       322       332     |
                                  291-MSE                                        338-MSE

   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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3K2A)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: HTH (544)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MEIS2_HUMAN | O14770)
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: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: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:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    GO:0003714    transcription corepressor activity    Interacting selectively and non-covalently with a repressing transcription factor and also with the basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    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:0001654    eye development    The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
    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:0045638    negative regulation of myeloid cell differentiation    Any process that stops, prevents, or reduces the frequency, rate or extent of myeloid cell differentiation.
    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:0031016    pancreas development    The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes.
    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:0070848    response to growth factor    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 growth factor stimulus.
    GO:0009612    response to mechanical stimulus    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 mechanical 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.
    GO:0008542    visual learning    Any process in an organism in which a change in behavior of an individual occurs in response to repeated exposure to a visual cue.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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        MEIS2_HUMAN | O147704xrm 5bng 5eg0

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