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(-) Description

Title :  HOMEOBOX TRANSCRIPTION FACTOR CDX2 BOUND TO METHYLATED DNA
 
Authors :  E. Morgunova, A. Popov, J. Taipale
Date :  07 Sep 16  (Deposition) - 31 May 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.66
Chains :  Asym. Unit :  A,B,E,F,K,M
Biol. Unit 1:  A,F,K  (1x)
Biol. Unit 2:  B,E,M  (1x)
Keywords :  Transcription, Transcription Factor, Methylated Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yin, E. Morgunova, A. Jolma, E. Kaasinen, B. Sahu, S. Khund-Sayeed, P. K. Das, T. Kivioja, K. Dave, F. Zhong, K. R. Nitta, M. Taipale, A. Popov, P. A. Ginno, S. Domcke, J. Yan, D. Schubeler, C. Vinson, J. Taipale
Impact Of Cytosine Methylation On Dna Binding Specificities Of Human Transcription Factors.
Science V. 356 2017
PubMed-ID: 28473536  |  Reference-DOI: 10.1126/SCIENCE.AAJ2239

(-) Compounds

Molecule 1 - DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM) P*GP*AP*CP*CP*TP*CP*C)-3')
    Chains: A, B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 2 - HOMEOBOX PROTEIN CDX-2
    Chains: K, M
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETG20A
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Expression System Vector Type: PLASMID
    Gene: CDX2, CDX3
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CDX-3,CAUDAL-TYPE HOMEOBOX PROTEIN 2
 
Molecule 3 - DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM) P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
    Chains: F, E
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABEFKM
Biological Unit 1 (1x): A  FK 
Biological Unit 2 (1x):  BE  M

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
15CM4Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 5LTY)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LTY)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys K:188 -Tyr K:189
2Lys M:188 -Tyr M:189

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) 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    
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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:DNA  Length:18
                                                  
                 5lty A   1 TTGTGTTTTAxGACCTCC  18
                                    10|       
                                     11-5CM   


Chain B from PDB  Type:DNA  Length:18
                                                  
                 5lty B   1 TTGTGTTTTAxGACCTCC  18
                                    10|       
                                     11-5CM   


Chain E from PDB  Type:DNA  Length:18
                                                  
                 5lty E  19 GGAGGTxGTAAAACACAA  36
                                  | 28        
                                 25-5CM       


Chain F from PDB  Type:DNA  Length:18
                                                  
                 5lty F  19 GGAGGTxGTAAAACACAA  36
                                  | 28        
                                 25-5CM       


Chain K from PDB  Type:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 5lty K 185 TKDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKERKINKKKLQQQQQQ 255
                                   194       204       214       224       234       244       254 


Chain M from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 5lty M 186 KDKYRVVYTDHQRLELEKEFHYSRYITIRRKAELAATLGLSERQVKIWFQNRRAKERKINKKKLQQQQQQ 255
                                   195       205       215       225       235       245       255
   Legend:   → Mismatch (orange background)
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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 5LTY)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LTY)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LTY)

(-) Gene Ontology  (36, 36)

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  Cis Peptide Bonds
    Lys K:188 - Tyr K:189   [ RasMol ]  
    Lys M:188 - Tyr M:189   [ RasMol ]  
 
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