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(-) Description

Title :  STRUCTURE OF LHX4 TRANSCRIPTION FACTOR COMPLEXED WITH DNA
 
Authors :  E. Morgunova, Y. Yin, A. Popov, J. Taipale
Date :  19 Jan 16  (Deposition) - 01 Feb 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.68
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription Factor, Complex With Dna, Dimer, 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 - LIM/HOMEOBOX PROTEIN LHX4
    ChainsA, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPETG20A
    Expression System Taxid469008
    Expression System VariantROSETTA
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 156-216
    GeneLHX4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymLIM HOMEOBOX PROTEIN 4
 
Molecule 2 - DNA (5'- D(P*AP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*CP*GP*TP*AP*AP*TP*TP*AP*G)-3')
    ChainsB
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES
 
Molecule 3 - DNA (5'- D(P*CP*TP*AP*AP*TP*TP*AP*CP*GP*CP*CP*TP*AP*AP*TP*TP*AP*GP*GP*T)-3')
    ChainsC
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5HOD)

(-) Sites  (0, 0)

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(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:143 -Lys A:144
2Pro D:88 -Arg D:89

 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/Biological 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
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Chain A from PDB  Type:PROTEIN  Length:61
                                                                                             
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                 5hod A  84 GAKRPRTTITAKQLETLKNAYKNSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 144
                                    93       103       113       123       133       143 

Chain B from PDB  Type:DNA  Length:20
                                                    
                 5hod B   1 ACCTAATTAGGCGTAATTAG  20
                                    10        20

Chain C from PDB  Type:DNA  Length:20
                                                    
                 5hod C  21 CTAATTACGCCTAATTAGGT  40
                                    30        40

Chain D from PDB  Type:PROTEIN  Length:58
                                                                                          
               SCOP domains ---------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 5hod D  87 RPRTTITAKQLETLKNAYKNSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLK 144
                                    96       106       116       126       136        

   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 5HOD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Leu A:143 - Lys A:144   [ RasMol ]  
    Pro D:88 - Arg D:89   [ RasMol ]  
 

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