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(-) Description

Title :  STRUCTURE OF HOXB13 COMPLEX WITH METHYLATED DNA
 
Authors :  E. Morgunova, Y. Yin, A. Jolma, A. Popov, J. Taipale
Date :  23 Oct 15  (Deposition) - 08 Feb 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,C,F  (1x)
Biol. Unit 2:  B,D,E  (1x)
Biol. Unit 3:  G,H,I  (1x)
Biol. Unit 4:  J,K,L  (1x)
Keywords :  Transcription Factor, Methylated Dna, Complex, Transcription (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 - HOMEOBOX PROTEIN HOX-B13
    Chains: A, B, G, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PETG20A
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA
    Fragment: UNP RESIDUES 217-278
    Gene: HOXB13
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM) P*GP*AP*GP*GP*TP*CP*C)-3')
    Chains: C, D, H, K
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*GP*GP*AP*CP*CP*TP*(5CM) P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')
    Chains: F, E, I, L
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): A C  F      
Biological Unit 2 (1x):  B DE       
Biological Unit 3 (1x):       GHI   
Biological Unit 4 (1x):          JKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
15CM8Mod. 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
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 5EF6)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EF6)

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Arg A:217 -Lys A:218
2Lys A:218 -Lys A:219
3Ala A:276 -Lys A:277
4Arg B:217 -Lys B:218
5Lys B:218 -Lys B:219
6Ala B:276 -Lys B:277
7Arg G:217 -Lys G:218
8Lys G:218 -Lys G:219
9Ala G:276 -Lys G:277
10Lys G:277 -Val G:278
11Arg J:217 -Lys J:218
12Lys J:218 -Lys J:219
13Ala J:276 -Lys J:277
14Lys J:277 -Val J:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5EF6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EF6)

(-) Exons   (0, 0)

(no "Exon" information available for 5EF6)

(-) 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:61
                                                                                             
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 5ef6 A 217 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKVLAK 277
                                   226       236       246       256       266       276 


Chain B from PDB  Type:PROTEIN  Length:61
                                                                                             
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 5ef6 B 217 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKVLAK 277
                                   226       236       246       256       266       276 


Chain C from PDB  Type:DNA  Length:18
                                                  
                 5ef6 C   1 TTGTGTTTTAxGAGGTCC  18
                                    10|       
                                     11-5CM   


Chain D from PDB  Type:DNA  Length:18
                                                  
                 5ef6 D   1 TTGTGTTTTAxGAGGTCC  18
                                    10|       
                                     11-5CM   


Chain E from PDB  Type:DNA  Length:18
                                                  
                 5ef6 E   1 GGACCTxGTAAAACACAA  18
                                  | 10        
                                  7-5CM       


Chain F from PDB  Type:DNA  Length:18
                                                  
                 5ef6 F   1 GGACCTxGTAAAACACAA  18
                                  | 10        
                                  7-5CM       


Chain G from PDB  Type:PROTEIN  Length:62
                                                                                              
               SCOP domains -------------------------------------------------------------- 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
                 5ef6 G 217 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKVLAKV 278
                                   226       236       246       256       266       276  


Chain H from PDB  Type:DNA  Length:18
                                                  
                 5ef6 H   1 TTGTGTTTTAxGAGGTCC  18
                                    10|       
                                     11-5CM   


Chain I from PDB  Type:DNA  Length:18
                                                  
                 5ef6 I   1 GGACCTxGTAAAACACAA  18
                                  | 10        
                                  7-5CM       


Chain J from PDB  Type:PROTEIN  Length:62
                                                                                              
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 5ef6 J 217 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKVLAKV 278
                                   226       236       246       256       266       276  


Chain K from PDB  Type:DNA  Length:18
                                                  
                 5ef6 K   1 TTGTGTTTTAxGAGGTCC  18
                                    10|       
                                     11-5CM   


Chain L from PDB  Type:DNA  Length:18
                                                  
                 5ef6 L   1 GGACCTxGTAAAACACAA  18
                                  | 10        
                                  7-5CM
   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 5EF6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EF6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EF6)

(-) Gene Ontology  (16, 16)

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  Cis Peptide Bonds
    Ala A:276 - Lys A:277   [ RasMol ]  
    Ala B:276 - Lys B:277   [ RasMol ]  
    Ala G:276 - Lys G:277   [ RasMol ]  
    Ala J:276 - Lys J:277   [ RasMol ]  
    Arg A:217 - Lys A:218   [ RasMol ]  
    Arg B:217 - Lys B:218   [ RasMol ]  
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    Arg J:217 - Lys J:218   [ RasMol ]  
    Lys A:218 - Lys A:219   [ RasMol ]  
    Lys B:218 - Lys B:219   [ RasMol ]  
    Lys G:218 - Lys G:219   [ RasMol ]  
    Lys G:277 - Val G:278   [ RasMol ]  
    Lys J:218 - Lys J:219   [ RasMol ]  
    Lys J:277 - Val J:278   [ RasMol ]  
 
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        HXB13_HUMAN | Q92826: 2cra 5edn 5eea 5eg0 5ego

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