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(-) Description

Title :  CRYSTAL STRUCTURE OF THE DM DOMAIN OF HUMAN DMRT1 BOUND TO 25MER TARGET DNA
 
Authors :  M. W. Murphy, J. K. Lee, S. Rojo, M. D. Gearhart, K. Kurahashi, S. Banerje G. Loeuille, A. Bashamboo, K. Mcelreavey, D. Zarkower, H. Aihara, V. J
Date :  02 Mar 15  (Deposition) - 27 May 15  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.81
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Transcription Factor, Protein-Dna Complex, Double Zn-Finger, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Murphy, J. K. Lee, S. Rojo, M. D. Gearhart, K. Kurahashi, S. Banerjee, G. A. Loeuille, A. Bashamboo, K. Mcelreavey, D. Zarkower H. Aihara, V. J. Bardwell
An Ancient Protein-Dna Interaction Underlying Metazoan Sex Determination.
Nat. Struct. Mol. Biol. V. 22 442 2015
PubMed-ID: 26005864  |  Reference-DOI: 10.1038/NSMB.3032

(-) Compounds

Molecule 1 - DOUBLESEX- AND MAB-3-RELATED TRANSCRIPTION FACTOR 1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PESUMOPRO
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 70-131
    Gene: DMRT1, DMT1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SPRLPKCARCRNHGYASPLKGHKRFCMWRDCQCKKCNLIAERQRVMAAQVALRRQQAQEEEL
    Synonym: DM DOMAIN EXPRESSED IN TESTIS PROTEIN 1
 
Molecule 2 - DNA (25-MER)
    Chains: D
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (25-MER)
    Chains: E
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric/Biological Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:82 , CYS A:100 , CYS A:102 , CYS A:105binding site for residue ZN A 201
2AC2SOFTWARECYS A:76 , CYS A:79 , HIS A:91 , CYS A:95binding site for residue ZN A 202
3AC3SOFTWAREHIS B:82 , CYS B:100 , CYS B:102 , CYS B:105binding site for residue ZN B 201
4AC4SOFTWARECYS B:76 , CYS B:79 , HIS B:91 , CYS B:95binding site for residue ZN B 202
5AC5SOFTWAREHIS C:82 , CYS C:100 , CYS C:102 , CYS C:105binding site for residue ZN C 201
6AC6SOFTWARECYS C:76 , CYS C:79 , HIS C:91 , CYS C:95binding site for residue ZN C 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YJ0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:74 -Lys A:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YJ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YJ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4YJ0)

(-) 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
(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:62
                                                                                              
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh.......................hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                 4yj0 A  70 SPRLPKCARCRNHGYASPLKGHKRFCMWRDCQCKKCNLIAERQRVMAAQVALRRQQAQEEEL 131
                                    79        89        99       109       119       129  


Chain B from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 4yj0 B  69 KSPRLPKCARCRNHGYASPLKGHKRFCMWRDCQCKKCNLIAERQRVMAAQVALRRQQAQEEEL 131
                                    78        88        98       108       118       128   


Chain C from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh......hhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 4yj0 C  69 KSPRLPKCARCRNHGYASPLKGHKRFCMWRDCQCKKCNLIAERQRVMAAQVALRRQQAQEEEL 131
                                    78        88        98       108       118       128   


Chain D from PDB  Type:DNA  Length:25
                                                         
                 4yj0 D   1 CGAGATTTGATACATTGTTGCTCGA  25
                                    10        20     


Chain E from PDB  Type:DNA  Length:25
                                                         
                 4yj0 E   1 TCGAGCAACAATGTATCAAATCTCG  25
                                    10        20
   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 4YJ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YJ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YJ0)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  4yj0
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