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(-) Description

Title :  HLRH-1 DNA BINDING DOMAIN - 12BP OCT4 PROMOTER COMPLEX
 
Authors :  M. L. Tuntland, E. A. Ortlund
Date :  27 Jul 16  (Deposition) - 09 Nov 16  (Release) - 05 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Lrh-1, Nuclear Receptor, Oct4, Dbd, 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 - NUCLEAR RECEPTOR SUBFAMILY 5 GROUP A MEMBER 2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMALCH10T
    Expression System Strain: BL21 DE3 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 79-187
    Gene: NR5A2, B1F, CPF, FTF
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-1-FETOPROTEIN TRANSCRIPTION FACTOR,B1-BINDING FACTOR, HB1F,CYP7A PROMOTER-BINDING FACTOR,HEPATOCYTIC TRANSCRIPTION FACTOR, LIVER RECEPTOR HOMOLOG 1,LRH-1
 
Molecule 2 - DNA (5'-D(*CP*TP*AP*GP*CP*CP*TP*TP*GP*AP*CP*C)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*GP*GP*TP*CP*AP*AP*GP*GP*CP*TP*AP*G)-3')
    Chains: B
    Engineered: YES
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:122 , CYS A:128 , CYS A:138 , CYS A:141binding site for residue ZN A 201
2AC2SOFTWARECYS A:86 , CYS A:89 , CYS A:103 , CYS A:106binding site for residue ZN A 202
3AC3SOFTWAREDT B:116 , DA B:117 , DG C:92binding site for residue GOL C 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L0M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L0M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L0M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L0M)

(-) Exons   (0, 0)

(no "Exon" information available for 5L0M)

(-) 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:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ............eee..eeehhhhhhhhhhhhhh.....................hhhhhhhhhhhh..hhhhh.............hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 5l0m A  83 EELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKRYTCIENQNCQIDKTQRKRCPYCRFQKCLSVGMKLEAVRADRMRGGRNKFGPMYKRDRAL 178
                                    92       102       112       122       132       142       152       162       172      


Chain B from PDB  Type:DNA  Length:12
                                            
                 5l0m B 107 GGTCAAGGCTAG 118
                                   116  


Chain C from PDB  Type:DNA  Length:12
                                            
                 5l0m C  89 CTAGCCTTGACC 100
                                    98
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  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 5L0M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L0M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L0M)

(-) Gene Ontology  (40, 40)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        NR5A2_HUMAN | O00482: 1yok 1yuc 1zdu 2a66 3plz 3tx7 4dor 4dos 4is8 4oni 4pld 4ple 4rwv 5l11 5syz 5unj

(-) Related Entries Specified in the PDB File

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