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(-) Description

Title :  STRUCTURE OF A TRANSCRIPTION FACTOR AND DNA COMPLEX
 
Authors :  T. Lian, Y. Xu, X. Su
Date :  21 Jul 16  (Deposition) - 10 May 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1:  G,I,K,L  (1x)
Biol. Unit 2:  A,B,C,D  (1x)
Biol. Unit 3:  E,F,H,J  (1x)
Biol. Unit 4:  M,N,O,P  (1x)
Keywords :  Transcription Factor, Dna, Complex, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Lian, Y. Xu, X. Su
Crystal Structure Of Tetrameric Arabidopsis Myc2 Reveals Th Mechanism Of Enhanced Interaction With Dna
Cell Rep 2017
PubMed: search

(-) Compounds

Molecule 1 - TRANSCRIPTION FACTOR MYC2
    Chains: G, I, A, B, E, F, M, N
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 446-525
    Gene: MYC2
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: ATMYC2,BASIC HELIX-LOOP-HELIX PROTEIN 6,BHLH 6,PROTEIN JASMONATE INSENSITIVE 1,R-HOMOLOGOUS ARABIDOPSIS PROTEIN 1,RAP-1, TRANSCRIPTION FACTOR EN 38,Z-BOX BINDING FACTOR 1 PROTEIN,BHLH TRANSCRIPTION FACTOR BHLH006,RD22BP1
 
Molecule 2 - DNA (5'-D(*AP*GP*GP*AP*AP*CP*AP*CP*GP*TP*GP*AP*CP*CP*C)- 3')
    Chains: K, C, H, O
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*GP*GP*GP*TP*CP*AP*CP*GP*TP*GP*TP*TP*CP*C)- 3')
    Chains: L, D, J, P
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678910111213141516
Asymmetric Unit : ABCDEFGHIJKLMNOP
Biological Unit 1 (1x):       G I KL    
Biological Unit 2 (1x): ABCD            
Biological Unit 3 (1x):     EF H J      
Biological Unit 4 (1x):             MNOP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5GNJ)

(-) Sites  (0, 0)

(no "Site" information available for 5GNJ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asn G:452 -His G:453
2Gly B:524 -Arg B:525
3Val N:478 -Ser N:479
4Ser N:479 -Lys N:480

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5GNJ)

(-) Sequences/Alignments

Asymmetric 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:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 5gnj A 452 NHVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINELKSKVVKTESEKLQIKNQLEEVKLELAGR 525
                                   461       471       481       491       501       511       521    


Chain B from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 5gnj B 449 EPLNHVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINELKSKVVKTESEKLQIKNQLEEVKLELAGR 525
                                   458       468       478       488       498       508       518       


Chain C from PDB  Type:DNA  Length:14
                                              
                 5gnj C 603 AGGAACACGTGACC 616
                                   612    


Chain D from PDB  Type:DNA  Length:14
                                              
                 5gnj D 804 GGGTCACGTGTTCC 817
                                   813    


Chain E from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5gnj E 452 NHVEAERQRREKLNQRFYALRAVVPNVKMDKASLLGDAIAYINELKSKVVKTESEKLQIKNQLEEVKLELAGR 525
                                   461       471      |482       492       502       512       522   
                                                    478|                                             
                                                     480                                             


Chain F from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5gnj F 452 NHVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINELKSKVVKTESEKLQIKNQLEEVKLELAG 524
                                   461       471       481       491       501       511       521   


Chain G from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5gnj G 452 NHVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINELKSKVVKTESEKLQIKNQLEEVKLELAG 524
                                   461       471       481       491       501       511       521   


Chain H from PDB  Type:DNA  Length:14
                                              
                 5gnj H 603 AGGAACACGTGACC 616
                                   612    


Chain I from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 5gnj I 449 EPLNHVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINELKSKVVKTESEKLQIKNQLEEVKLELA 523
                                   458       468       478       488       498       508       518     


Chain J from PDB  Type:DNA  Length:13
                                             
                 5gnj J 805 GGTCACGTGTTCC 817
                                   814   


Chain K from PDB  Type:DNA  Length:14
                                              
                 5gnj K 603 AGGAACACGTGACC 616
                                   612    


Chain L from PDB  Type:DNA  Length:14
                                              
                 5gnj L 804 GGGTCACGTGTTCC 817
                                   813    


Chain M from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5gnj M 452 NHVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINELKSKVVKTESEKLQIKNQLEEVKLELAG 524
                                   461       471       481       491       501       511       521   


Chain N from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5gnj N 452 NHVEAERQRREKLNQRFYALRAVVPNVSKMDKASLLGDAIAYINELKSKVVKTESEKLQIKNQLEEVKLELAG 524
                                   461       471       481       491       501       511       521   


Chain O from PDB  Type:DNA  Length:13
                                             
                 5gnj O 604 GGAACACGTGACC 616
                                   613   


Chain P from PDB  Type:DNA  Length:12
                                            
                 5gnj P 805 GGTCACGTGTTC 816
                                   814
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5GNJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn G:452 - His G:453   [ RasMol ]  
    Gly B:524 - Arg B:525   [ RasMol ]  
    Ser N:479 - Lys N:480   [ RasMol ]  
    Val N:478 - Ser N:479   [ RasMol ]  
 
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  5gnj
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  MYC2_ARATH | Q39204
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