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(-) Description

Title :  TRANSCRIPTION FACTOR GRDBD AND SMGRE COMPLEX
 
Authors :  X. D. Su, T. Lian, J. Jin
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 :  J. Jin, T. Lian, X. D. Su
The Effects Of Cytosine Methylation On General Transcriptio Factors
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM) P*AP*TP*CP*AP*TP*GP*TP*TP*(5CM)P*TP*G)-3')
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 2 - 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 3 - DNA (5'-D(*CP*CP*AP*GP*AP*AP*(5CM) P*AP*TP*GP*AP*TP*GP*TP*TP*(5CM)P*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, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
15CM4Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
2ZN4Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
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
5AC5SOFTWAREARG B:466 , DG C:13 , DT C:14 , DT C:15 , HOH C:109 , HOH C:116 , DA D:31 , DA D:34 , HOH D:106 , HOH D:109 , HOH D:110binding site for Di-nucleotide DA D 32 and 5CM D 33
6AC6SOFTWAREDA C:11 , DT C:12 , DG C:13 , HOH C:109 , DA D:32 , DT D:35 , HOH D:103 , HOH D:106 , HOH D:109binding site for Di-nucleotide 5CM D 33 and DA D 34
7AC7SOFTWAREDA C:3 , DG C:4 , DA C:5 , DA C:6 , DT D:40 , DT D:43 , HOH D:104 , HOH D:111 , HOH D:114binding site for Di-nucleotide DT D 41 and 5CM D 42
8AC8SOFTWAREDC C:2 , DA C:3 , DG C:4 , DA C:5 , DC D:27 , DT D:41 , DG D:44 , HOH D:104 , HOH D:107 , HOH D:111 , HOH D:114binding site for Di-nucleotide 5CM D 42 and DT D 43

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EMC)

(-) 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:70
                                                                                                      
               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
                 5emc A 438 KLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNL 507
                                   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
                 5emc B 437 PKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLE 508
                                   446       456       466       476       486       496       506  


Chain C from PDB  Type:DNA  Length:18
                                                  
                 5emc C   1 CCAGAAxATCATGTTxTG  18
                                  | 10     |  
                                  7-5CM   16-5CM


Chain D from PDB  Type:DNA  Length:18
                                                  
                 5emc D  27 CCAGAAxATGATGTTxTG  44
                                  | 36     |  
                                 33-5CM   42-5CM
   Legend:   → Mismatch (orange background)
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    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5EMC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 37)

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
        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 5emp 5emq 5g3j 5g5w

(-) Related Entries Specified in the PDB File

5emp 5emq