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(-) Description

Title :  TRANSCRIPTION FACTOR GRDBD AND MMGRE COMPLEX
 
Authors :  T. Lian, J. Jin, X. Su
Date :  06 Nov 15  (Deposition) - 29 Jun 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription Factor, Complex, Dna, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Lian, J. Jin, X. Su
The Effects Of Cytosine Methylation On General Transcriptio Factors
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUCOCORTICOID RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI-PICHIA PASTORIS SHUTTLE VECTOR PPPHIS4
    Expression System Taxid: 1182038
    Fragment: UNP RESIDUES 411-500
    Gene: NR3C1, GRL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GR,NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 1
 
Molecule 2 - DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*GP*AP*TP*GP*TP*TP*CP*TP*G)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(P*CP*CP*AP*GP*AP*AP*CP*AP*TP*(5CM) P*AP*TP*GP*TP*TP*CP*TP*G)-3')
    Chains: D
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:440 , CYS A:443 , CYS A:457 , CYS A:460binding site for residue ZN A 601
2AC2SOFTWARECYS A:476 , CYS A:482 , CYS A:492 , CYS A:495binding site for residue ZN A 602
3AC3SOFTWARECYS B:440 , CYS B:443 , CYS B:457 , CYS B:460binding site for residue ZN B 601
4AC4SOFTWARECYS B:476 , CYS B:482 , CYS B:492 , CYS B:495binding site for residue ZN B 602
5AC5SOFTWAREDT C:9 , DG C:10 , DA C:11 , DA D:9 , DA D:12binding site for Di-nucleotide DT D 10 and 5CM D 11
6AC6SOFTWAREDT C:9 , DG C:10 , DA C:11 , DT D:10 , DT D:13binding site for Di-nucleotide 5CM D 11 and DA D 12

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EMP)

(-) 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:PROTEIN  Length:71
                                                                                                       
               SCOP domains ----------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee..eeehhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------- Transcript
                 5emp A 438 KLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLE 508
                                   447       457       467       477       487       497       507 


Chain B from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eee..eeehhhhhhhhhhhhhh.....................hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 5emp B 438 KLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 509
                                   447       457       467       477       487       497       507  


Chain C from PDB  Type:DNA  Length:18
                                                  
                 5emp C   1 CCAGAACATGATGTTCTG  18
                                    10        


Chain D from PDB  Type:DNA  Length:18
                                                  
                 5emp D   2 CCAGAACATxATGTTCTG  19
                                    11        
                                    11-5CM
   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 5EMP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  5emp
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 Related Entries

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

UniProtKB/Swiss-Prot
        GCR_HUMAN | P04150: 1m2z 1nhz 1p93 3bqd 3cld 3e7c 3h52 3k22 3k23 4csj 4hn5 4hn6 4lsj 4mdd 4p6w 4p6x 4udc 4udd 5cbx 5cby 5cbz 5cc1 5e69 5e6a 5e6b 5e6c 5e6d 5emc 5emq 5g3j 5g5w

(-) Related Entries Specified in the PDB File

5emc 5emq