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(-) Description

Title :  SOLUTION NMR STRUCTURE OF SLED DOMAIN OF SCML2
 
Authors :  I. Bezsonova
Date :  24 Sep 13  (Deposition) - 23 Apr 14  (Release) - 18 Jun 14  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Prc1, Pcg, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Bezsonova
Solution Nmr Structure Of The Dna-Binding Domain From Scml2 (Sex Comb On Midleg-Like 2).
J. Biol. Chem. V. 289 15739 2014
PubMed-ID: 24727478  |  Reference-DOI: 10.1074/JBC.M113.524009

(-) Compounds

Molecule 1 - SEX COMB ON MIDLEG-LIKE PROTEIN 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET28B
    Fragment: UNP RESIDUES 354-468
    Gene: SCML2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x): A
NMR Structure * (1x): A

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2MEM)

(-) Sites  (0, 0)

(no "Site" information available for 2MEM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2MEM)

(-) Cis Peptide Bonds  (2, 40)

NMR Structure
No.ModelResidues
11, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gly A:368 -Pro A:369
21, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20Gly A:384 -Pro A:385

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2MEM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2MEM)

(-) Exons   (3, 3)

NMR Structure (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002519001aENSE00001341544X:18372847-18372712136SCML2_HUMAN-00--
1.2ENST000002519002ENSE00002195410X:18352215-1835217046SCML2_HUMAN1-880--
1.3ENST000002519003ENSE00001740872X:18348775-1834870769SCML2_HUMAN8-31240--
1.4ENST000002519004ENSE00001722015X:18343097-1834302771SCML2_HUMAN31-54240--
1.5ENST000002519005ENSE00001761590X:18342213-18341979235SCML2_HUMAN55-133790--
1.6ENST000002519006ENSE00001802908X:18338540-1833845289SCML2_HUMAN133-162300--
1.7ENST000002519007ENSE00001780951X:18323335-18323092244SCML2_HUMAN163-244820--
1.8ENST000002519008ENSE00001602863X:18283922-18283705218SCML2_HUMAN244-316730--
1.9ENST000002519009ENSE00001692459X:18278411-18278291121SCML2_HUMAN317-357411A:350-357 (gaps)10
1.10ENST0000025190010ENSE00001801055X:18276367-18276164204SCML2_HUMAN357-425691A:357-42569
1.11ENST0000025190011ENSE00001720943X:18275150-18274968183SCML2_HUMAN425-486621A:425-46844
1.12bENST0000025190012bENSE00001776891X:18266002-18265889114SCML2_HUMAN486-524390--
1.13ENST0000025190013ENSE00001632032X:18264948-18264697252SCML2_HUMAN524-608850--
1.14ENST0000025190014ENSE00000666137X:18260710-18260559152SCML2_HUMAN608-658510--
1.15bENST0000025190015bENSE00001765000X:18259499-182574342066SCML2_HUMAN659-700420--

(-) 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:119
 aligned with SCML2_HUMAN | Q9UQR0 from UniProtKB/Swiss-Prot  Length:700

    Alignment length:121
                                   357       367       377       387       397       407       417       427       437       447       457       467 
          SCML2_HUMAN   348 GPCKIVMSTVCVYVNKHGNFGPHLDPKRIQQLPDHFGPGPVNVVLRRIVQACVDCALETKTVFGYLKPDNRGGEVITASFDGETHSIQLPPVNSASFALRFLENFCHSLQCDNLLSSQPFS 468
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .--.....eeee............hhhhhhhh...eeeeehhhhhhhhhhhhhhhh.hhhhhh...........eeeeee..eeeeee.....hhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) ---------Exon 1.10  PDB: A:357-425 UniProt: 357-425                           ------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  -------------------------------------------------------------------Exon 1.11  PDB: A:425-468 UniProt: 425-486   Transcript 1 (2)
                 2mem A 350 G--SHMMSTVCVYVNKHGNFGPHLDPKRIQQLPDHFGPGPVNVVLRRIVQACVDCALETKTVFGYLKPDNRGGEVITASFDGETHSIQLPPVNSASFALRFLENFCHSLQCDNLLSSQPFS 468
                            |  |   357       367       377       387       397       407       417       427       437       447       457       467 
                            |  |                                                                                                                     
                          350  |                                                                                                                     
                             351
   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  (0, 0)

(no "SCOP Domain" information available for 2MEM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2MEM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2MEM)

(-) Gene Ontology  (7, 7)

NMR Structure(hide GO term definitions)
Chain A   (SCML2_HUMAN | Q9UQR0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    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.
biological process
    GO:0009653    anatomical structure morphogenesis    The process in which anatomical structures are generated and organized. Morphogenesis pertains to the creation of form.
    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:0031519    PcG protein complex    A chromatin-associated multiprotein complex containing Polycomb Group proteins. In Drosophila, Polycomb group proteins are involved in the long-term maintenance of gene repression, and PcG protein complexes associate with Polycomb group response elements (PREs) in target genes to regulate higher-order chromatin structure.
    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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  Cis Peptide Bonds
    Gly A:368 - Pro A:369   [ RasMol ]  
    Gly A:384 - Pro A:385   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        SCML2_HUMAN | Q9UQR0: 1oi1 2biv 2vyt 4edu

(-) Related Entries Specified in the PDB File

1oi1 MBT DOMAINS OF SCML2
2biv MBT DOMAINS OF SCML2
2vyt MBT DOMAINS OF SCML2
4edu MBT DOMAINS OF SCML2 RELATED ID: 19526 RELATED DB: BMRB