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(-) Description

Title :  STRUCTURE OF LIN54 TESMIN DOMAIN BOUND TO DNA
 
Authors :  A. H. Marceau, J. G. Felthousen, P. D. Goetsch, H. Lee, S. M. Tripathi, S. L. Litovchick, S. M. Rubin
Date :  15 Dec 15  (Deposition) - 03 Aug 16  (Release) - 10 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym. Unit :  A,B,C,D,H,I
Biol. Unit 1:  A,H,I  (1x)
Biol. Unit 2:  B,C,D  (1x)
Keywords :  Transcription Factor, Tesmin Domain, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. H. Marceau, J. G. Felthousen, P. D. Goetsch, A. N. Iness, H. W. Lee, S. M. Tripathi, S. Strome, L. Litovchick, S. M. Rubin
Structural Basis For Lin54 Recognition Of Chr Elements In Cell Cycle-Regulated Promoters.
Nat Commun V. 7 12301 2016
PubMed-ID: 27465258  |  Reference-DOI: 10.1038/NCOMMS12301

(-) Compounds

Molecule 1 - PROTEIN LIN-54 HOMOLOG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEV
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: TESMIN DOMAIN (UNP RESIDUES 515-646)
    Gene: LIN54, CXCDC1, KIAA2037
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CXC DOMAIN-CONTAINING PROTEIN 1
 
Molecule 2 - DNA (5'-D(*GP*AP*GP*TP*TP*TP*GP*AP*AP*AP*CP*T)-3')
    Chains: C, H
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*CP*AP*GP*TP*TP*TP*CP*AP*AP*AP*CP*TP*C)-3')
    Chains: D, I
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDHI
Biological Unit 1 (1x): A   HI
Biological Unit 2 (1x):  BCD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric Unit (1, 12)
No.NameCountTypeFull Name
1ZN12Ligand/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  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:525 , CYS A:527 , CYS A:532 , CYS A:537 , ZN A:702binding site for residue ZN A 701
02AC2SOFTWARECYS A:525 , CYS A:532 , CYS A:546 , CYS A:551 , CYS A:554 , ZN A:701 , ZN A:703binding site for residue ZN A 702
03AC3SOFTWARECYS A:525 , CYS A:539 , CYS A:546 , CYS A:549 , ZN A:702binding site for residue ZN A 703
04AC4SOFTWARECYS A:599 , CYS A:601 , CYS A:606 , CYS A:611 , ZN A:705 , ZN A:706binding site for residue ZN A 704
05AC5SOFTWARECYS A:599 , CYS A:606 , CYS A:620 , CYS A:626 , CYS A:629 , ZN A:704binding site for residue ZN A 705
06AC6SOFTWARECYS A:599 , CYS A:613 , CYS A:620 , CYS A:624 , ZN A:704binding site for residue ZN A 706
07AC7SOFTWARECYS B:525 , CYS B:527 , CYS B:532 , CYS B:537 , ZN B:702binding site for residue ZN B 701
08AC8SOFTWARECYS B:525 , CYS B:532 , CYS B:546 , CYS B:551 , CYS B:554 , ZN B:701binding site for residue ZN B 702
09AC9SOFTWARECYS B:525 , CYS B:539 , CYS B:546 , CYS B:549binding site for residue ZN B 703
10AD1SOFTWARECYS B:599 , CYS B:601 , CYS B:606 , CYS B:611 , ZN B:705 , ZN B:706binding site for residue ZN B 704
11AD2SOFTWARECYS B:599 , CYS B:606 , CYS B:620 , CYS B:626 , CYS B:629 , ZN B:704binding site for residue ZN B 705
12AD3SOFTWARECYS B:599 , CYS B:613 , CYS B:620 , CYS B:624 , ZN B:704binding site for residue ZN B 706

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FD3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FD3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FD3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FD3)

(-) Exons   (0, 0)

(no "Exon" information available for 5FD3)

(-) 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:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhh..............hhhhhhhhhhhhhhhhhhh.....................hhhhhh..................hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5fd3 A 522 RKPCNCTKSLCLKLYCDCFANGEFCNNCNCTNCYNNLEHENERQKAIKACLDRNPEAFKPKKGCNCKRSGCLKNYCECYEAKIMCSSICKCIGCKNFEESPERKTLMH 643
                                   531       541       551       561       571       581||     605       615       625       635        
                                                                                      582|                                              
                                                                                       597                                              


Chain B from PDB  Type:PROTEIN  Length:108
                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............hhhhhh..............hhhhhhhhhhhhhhhhhhh....................hhhhhh..................hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------ Transcript
                 5fd3 B 522 RKPCNCTKSLCLKLYCDCFANGEFCNNCNCTNCYNNLEHENERQKAIKACLDRNPEAFKPKGCNCKRSGCLKNYCECYEAKIMCSSICKCIGCKNFEESPERKTLMHL 644
                                   531       541       551       561       571       581|      606       616       626       636        
                                                                                     581|                                               
                                                                                      597                                               


Chain C from PDB  Type:DNA  Length:12
                                            
                 5fd3 C   1 GAGTTTGAAACT  12
                                    10  


Chain D from PDB  Type:DNA  Length:13
                                             
                 5fd3 D   1 CAGTTTCAAACTC  13
                                    10   


Chain H from PDB  Type:DNA  Length:12
                                            
                 5fd3 H   1 GAGTTTGAAACT  12
                                    10  


Chain I from PDB  Type:DNA  Length:13
                                             
                 5fd3 I   1 CAGTTTCAAACTC  13
                                    10
   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 5FD3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FD3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FD3)

(-) Gene Ontology  (8, 8)

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  5fd3
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