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(-) Description

Title :  GCNF DNA BINDING DOMAIN - OCT4 DR0 COMPLEX
 
Authors :  E. R. Weikum, E. A. Ortlund
Date :  07 Jul 16  (Deposition) - 09 Nov 16  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,E,G
Keywords :  Nuclear Receptor, Transcription Factor, Dna Binding, Development, Protein-Dna Complex, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. R. Weikum, M. L. Tuntland, M. N. Murphy, E. A. Ortlund
A Structural Investigation Into Oct4 Regulation By Orphan Nuclear Receptors, Germ Cell Nuclear Factor (Gcnf), And Liver Receptor Homolog-1 (Lrh-1).
J. Mol. Biol. V. 428 4981 2016
PubMed-ID: 27984042  |  Reference-DOI: 10.1016/J.JMB.2016.10.025

(-) Compounds

Molecule 1 - DNA (5'-D(*AP*GP*AP*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*GP*A)- 3')
    Chains: A
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synthetic: YES
 
Molecule 2 - NUCLEAR RECEPTOR SUBFAMILY 6 GROUP A MEMBER 1
    Chains: B, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: LIC MBP
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Variant: PLYSS
    Expression System Vector Type: PMCSG7
    Gene: NR6A1, GCNF
    Mutation: YES
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: GERM CELL NUCLEAR FACTOR,MGCNF,RETINOID RECEPTOR-RELATED TESTIS-SPECIFIC RECEPTOR,RTR
 
Molecule 3 - DNA (5'-D(*TP*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*CP*TP*CP*T)- 3')
    Chains: E
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEG

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS B:75 , CYS B:78 , CYS B:92 , CYS B:95binding site for residue ZN B 201
2AC2SOFTWARECYS B:111 , CYS B:117 , CYS B:127 , CYS B:130binding site for residue ZN B 202
3AC3SOFTWARECYS G:75 , CYS G:78 , CYS G:92 , CYS G:95binding site for residue ZN G 201
4AC4SOFTWARECYS G:111 , CYS G:117 , CYS G:127 , CYS G:130binding site for residue ZN G 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KRB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5KRB)

(-) 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    
   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:DNA  Length:16
                                                
                 5krb A 105 AGAGGTCAAGGCTAGA 120
                                   114      


Chain B from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee..ee.hhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh.hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5krb B  72 QRTCLICGDRATGLHYGIISCEGCKGFFKRSISNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAI 145
                                    81        91       101       111       121       131       141    


Chain E from PDB  Type:DNA  Length:16
                                                
                 5krb E  89 TCTAGCCTTGACCTCT 104
                                    98      


Chain G from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eee..eeehhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh.hhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 5krb G  74 TCLICGDRATGLHYGIISCEGCKGFFKRSISNKRVYRCSRDKNCVMSRKQRNRCQYCRLLKCLQMGMNRKAIREDGMPGGRN 155
                                    83        93       103       113       123       133       143       153
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5KRB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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