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(-) Description

Title :  STRUCTURAL BASIS OF TRANSCRIPTIONAL GENE SILENCING MEDIATED BY ARABIDOPSIS MOM1
 
Authors :  T. Nishikura, T. J. Petty, T. Halazonetis, J. Paszkowski, S. Thore
Date :  09 Jan 12  (Deposition) - 07 Mar 12  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Coiled-Coil, Hendecad, Transcriptional Gene Silencing, Sirna, Nucleus, Chromatin, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Nishimura, G. Molinard, T. J. Petty, L. Broger, C. Gabus, T. D. Halazonetis, S. Thore, J. Paszkowski
Structural Basis Of Transcriptional Gene Silencing Mediated By Arabidopsis Mom1.
Plos Genet. V. 8 02484 2012
PubMed-ID: 22346760  |  Reference-DOI: 10.1371/JOURNAL.PGEN.1002484

(-) Compounds

Molecule 1 - HELICASE PROTEIN MOM1
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: CONSERVED MOM1 MOTIF 2 (CMM2)
    Gene: MOM1, MOM, AT1G08060, T6D22.14
    Organism Common: MOUSE-EAR CRESS,THALE-CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: PROTEIN MAINTENANCE OF METHYLATION, PROTEIN MORPHEUS MOLECULE 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3VEM)

(-) Sites  (0, 0)

(no "Site" information available for 3VEM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3VEM)

(-) 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:82
 aligned with MOM1_ARATH | Q9M658 from UniProtKB/Swiss-Prot  Length:2001

    Alignment length:82
                                  1741      1751      1761      1771      1781      1791      1801      1811  
          MOM1_ARATH   1732 FNDPFLHELEKLRRESENSKKTFEEKKSILKAELERKMAEVQAEFRRKFHEVEAEHNTRTTKIEKDKNLVIMNKLLANAFLS 1813
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                3vem A 1732 FNDPFLHELEKLRRESENSKKTFEEKKSILKAELERKMAEVQAEFRRKFHEVEAEHNTRTTKIEKDKNLVIMNKLLANAFLS 1813
                                  1741      1751      1761      1771      1781      1791      1801      1811  


Chain B from PDB  Type:PROTEIN  Length:82
 aligned with MOM1_ARATH | Q9M658 from UniProtKB/Swiss-Prot  Length:2001

    Alignment length:82
                                  1741      1751      1761      1771      1781      1791      1801      1811  
          MOM1_ARATH   1732 FNDPFLHELEKLRRESENSKKTFEEKKSILKAELERKMAEVQAEFRRKFHEVEAEHNTRTTKIEKDKNLVIMNKLLANAFLS 1813
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                3vem B 1732 FNDPFLHELEKLRRESENSKKTFEEKKSILKAELERKMAEVQAEFRRKFHEVEAEHNTRTTKIEKDKNLVIMNKLLANAFLS 1813
                                  1741      1751      1761      1771      1781      1791      1801      1811  


Chain C from PDB  Type:PROTEIN  Length:83
 aligned with MOM1_ARATH | Q9M658 from UniProtKB/Swiss-Prot  Length:2001

    Alignment length:83
                                  1738      1748      1758      1768      1778      1788      1798      1808   
          MOM1_ARATH   1729 FPVFNDPFLHELEKLRRESENSKKTFEEKKSILKAELERKMAEVQAEFRRKFHEVEAEHNTRTTKIEKDKNLVIMNKLLANAF 1811
               SCOP domains ----------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------- Transcript
                3vem C 1729 FPVFNDPFLHELEKLRRESENSKKTFEEKKSILKAELERKMAEVQAEFRRKFHEVEAEHNTRTTKIEKDKNLVIMNKLLANAF 1811
                                  1738      1748      1758      1768      1778      1788      1798      1808   


Chain D from PDB  Type:PROTEIN  Length:80
 aligned with MOM1_ARATH | Q9M658 from UniProtKB/Swiss-Prot  Length:2001

    Alignment length:80
                                  1741      1751      1761      1771      1781      1791      1801      1811
          MOM1_ARATH   1732 FNDPFLHELEKLRRESENSKKTFEEKKSILKAELERKMAEVQAEFRRKFHEVEAEHNTRTTKIEKDKNLVIMNKLLANAF 1811
               SCOP domains -------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------- Transcript
                3vem D 1732 FNDPFLHELEKLRRESENSKKTFEEKKSILKAELERKMAEVQAEFRRKFHEVEAEHNTRTTKIEKDKNLVIMNKLLANAF 1811
                                  1741      1751      1761      1771      1781      1791      1801      1811
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (0, 0)

(no "SCOP Domain" information available for 3VEM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VEM)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MOM1_ARATH | Q9M658)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0006344    maintenance of chromatin silencing    The maintenance of chromatin in a transcriptionally silent state such as heterochromatin.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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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