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(-) Description

Title :  CRYSTAL STRUCTURE OF AFT2 IN COMPLEX WITH DNA
 
Authors :  C. B. Poor, R. Sanishvili, J. P. Schuermann, C. He
Date :  10 Jul 13  (Deposition) - 05 Mar 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,D,G,H  (1x)
Biol. Unit 2:  B,C,E,F  (1x)
Keywords :  Wrky-Gcm1, Transcription Factor, Dna Binding, Iron Binding, Transcription Activator-Dna Complex, Wrky-Gcm1 Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. B. Poor, S. V. Wegner, H. Li, A. C. Dlouhy, J. P. Schuermann, R. Sanishvili, J. R. Hinshaw, P. J. Riggs-Gelasco, C. E. Outten, C. He
Molecular Mechanism And Structure Of The Saccharomyces Cerevisiae Iron Regulator Aft2.
Proc. Natl. Acad. Sci. Usa V. 111 4043 2014
PubMed-ID: 24591629  |  Reference-DOI: 10.1073/PNAS.1318869111

(-) Compounds

Molecule 1 - IRON-REGULATED TRANSCRIPTIONAL ACTIVATOR AFT2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 38-193
    Gene: AFT2, YPL202C
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: ATCC 204508 / S288C
    Synonym: ACTIVATOR OF IRON TRANSCRIPTION PROTEIN 2
 
Molecule 2 - 5'-D(*TP*AP*AP*TP*GP*GP*GP*TP*GP*CP*AP*CP*T)-3'
    Chains: E, G
    Engineered: YES
    Other Details: PROMOTER REGION FRAGMENT
    Synthetic: YES
 
Molecule 3 - 5'-D(*AP*AP*GP*TP*GP*CP*AP*CP*CP*CP*AP*TP*T)-3'
    Chains: F, H
    Engineered: YES
    Other Details: PROMOTER REGION FRAGMENT
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A  D  GH
Biological Unit 2 (1x):  BC EF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ZN6Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:86 , CYS A:109 , HIS A:133 , HIS A:135BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS B:86 , CYS B:109 , HIS B:133 , HIS B:135BINDING SITE FOR RESIDUE ZN B 201
3AC3SOFTWAREASP B:53 , HIS B:55 , HOH B:301BINDING SITE FOR RESIDUE ZN B 202
4AC4SOFTWARECYS C:86 , CYS C:109 , HIS C:133 , HIS C:135BINDING SITE FOR RESIDUE ZN C 201
5AC5SOFTWARECYS D:86 , CYS D:109 , HIS D:133 , HIS D:135BINDING SITE FOR RESIDUE ZN D 201
6AC6SOFTWAREASP D:53 , HIS D:55 , HOH D:301 , HOH D:302BINDING SITE FOR RESIDUE ZN D 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LMG)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Asp A:46 -Pro A:47
2Asp B:46 -Pro B:47
3Asp C:46 -Pro C:47
4Asp D:46 -Pro D:47

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LMG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LMG)

(-) Exons   (0, 0)

(no "Exon" information available for 4LMG)

(-) 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:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........hhhhhhhhhhhhhhhhh..eeeeeee..eeeeee.......eeeeeee....eeeeeee........hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lmg A  42 LIHLDPVPSFEDRHEIKPWLQKIFYPQGIDIVIERSDSSKVTFKCRSVACPFRIRAAYSVRLQKWNVVVMNNIHSHELRFDLITKTDDYKKFKENLRQKNDEKAIKTFDELEYKASLNLP 179
                                    51        61        71        81       109       119       129       139       149       159       169       179
                                                                          89|                                                                       
                                                                          108                                                                       


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...........hhhhhhhhhhhhhh..eeeeee...eeeeee.......eeeeeee....eeeeeee........hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lmg B  42 LIHLDPVPSFEDRHEIKPWLQKIFYPQGIDIVIERSDSSKVTFKCRSVACPFRIRAAYSVRLQKWNVVVMNNIHSHELRFDLITKTDDYKKFKENLRQKNDEKAIKTFDELEYKASLNLPL 180
                                    51        61        71        81       109       119       129       139       149       159       169       179 
                                                                          89|                                                                        
                                                                          108                                                                        


Chain C from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........hhhhhhhhhhhhhhhhh..eeeeeee..eeeeee.......eeeeeee....eeeeeeee.......hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lmg C  42 LIHLDPVPSFEDRHEIKPWLQKIFYPQGIDIVIERSDSSKVTFKCRSVACPFRIRAAYSVRLQKWNVVVMNNIHSHELRFDLITKTDDYKKFKENLRQKNDEKAIKTFDELEYKASLNLPL 180
                                    51        61        71        81       109       119       129       139       149       159       169       179 
                                                                          89|                                                                        
                                                                          108                                                                        


Chain D from PDB  Type:PROTEIN  Length:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........hhhhhhhhhhhhhhhhh..eeeeeee..eeeeee......eeeeeee....eeeeeee........hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lmg D  42 LIHLDPVPSFEDRHEIKPWLQKIFYPQGIDIVIERSDSSKVTFKCRSACPFRIRAAYSVRLQKWNVVVMNNIHSHELRFDLITKTDDYKKFKENLRQKNDEKAIKTFDELEYKASLNLPL 180
                                    51        61        71        81      |110       120       130       140       150       160       170       180
                                                                         88|                                                                        
                                                                         108                                                                        


Chain E from PDB  Type:DNA  Length:13
                                             
                 4lmg E   1 TAATGGGTGCACT  13
                                    10   


Chain F from PDB  Type:DNA  Length:12
                                            
                 4lmg F  15 AGTGCACCCATT  26
                                    24  


Chain G from PDB  Type:DNA  Length:13
                                             
                 4lmg G   1 TAATGGGTGCACT  13
                                    10   


Chain H from PDB  Type:DNA  Length:13
                                             
                 4lmg H  14 AAGTGCACCCATT  26
                                    23
   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 4LMG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LMG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LMG)

(-) Gene Ontology  (10, 10)

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