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(-) Description

Title :  ICP4 DNA-BINDING DOMAIN IN COMPLEX WITH 19MER DNA DUPLEX FROM ITS OWN PROMOTER
 
Authors :  R. B. Tunnicliffe, M. P. Lockhart-Cairns, C. Levy, P. Mould, T. A. Jowit C. Baldock, R. M. Sandri-Goldin, A. P. Golovanov
Date :  24 Nov 16  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,J
Biol. Unit 1:  C,D,G,H,J  (1x)
Biol. Unit 2:  A,B,E,F  (1x)
Keywords :  Transcription Factor, Herpes Virus, Intercalation, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. B. Tunnicliffe, M. P. Lockhart-Cairns, C. Levy, A. P. Mould, T. A. Jowitt, H. Sito, C. Baldock, R. M. Sandri-Goldin, A. P. Golovanov
The Herpes Viral Transcription Factor Icp4 Forms A Novel Dn Recognition Complex.
Nucleic Acids Res. 2017
PubMed-ID: 28505309  |  Reference-DOI: 10.1093/NAR/GKX419

(-) Compounds

Molecule 1 - DNA (5'- D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
    Chains: G, E
    Engineered: YES
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Other Details: SYNTHETIC DNA, SEQUENCES MATCHES A REGION FROM THE ICP4 PROMOTER (IE3)
    Synthetic: YES
 
Molecule 2 - DNA (5'- D(*GP*CP*TP*CP*CP*GP*TP*GP*TP*GP*GP*AP*CP*GP*AP*TP*CP*GP*G)-3')
    Chains: H, F
    Engineered: YES
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Other Details: SYNTHETIC DNA, SEQUENCES MATCHES A REGION FROM THE ICP4 PROMOTER (IE3)
    Synthetic: YES
 
Molecule 3 - RS1
    Chains: A, C, D, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: T7 EXPRESS LYSY
    Expression System Plasmid: PET-21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HHV-1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Other Details: DNA BINDING DOMAIN OF ICP4, RESIDUES 258-487
 
Molecule 4 - ICP4 DNA BINDING DOMAIN
    Chains: J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: T7 EXPRESS LYSY
    Expression System Plasmid: PET-21A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LIKELY N-TERMINUS OF CHAIN D, BUT CHAIN CONNECTIVITY IS AMBIGUOUS
    Organism Common: HHV-1
    Organism Scientific: HUMAN HERPESVIRUS 1
    Organism Taxid: 10298
    Other Details: DNA BINDING DOMAIN OF ICP4, RESIDUES 258-487

 Structural Features

(-) Chains, Units

  123456789
Asymmetric Unit : ABCDEFGHJ
Biological Unit 1 (1x):   CD  GHJ
Biological Unit 2 (1x): AB  EF   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2MG1Ligand/IonMAGNESIUM ION
3SO47Ligand/IonSULFATE ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3SO43Ligand/IonSULFATE ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3SO44Ligand/IonSULFATE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDC H:1 , DC H:2binding site for residue MG H 101
2AC2SOFTWAREPRO A:383 , ASP A:384 , ARG A:471binding site for residue SO4 A 501
3AC3SOFTWARELEU A:391 , GLN A:392 , ALA A:426 , ARG A:427 , MET A:454 , HOH A:606binding site for residue SO4 A 502
4AC4SOFTWARESER C:312binding site for residue CL C 501
5AC5SOFTWAREPRO C:383 , ASP C:384 , ARG C:471 , HOH C:619binding site for residue SO4 C 502
6AC6SOFTWARELEU C:391 , ARG C:427 , MET C:454 , HOH C:631binding site for residue SO4 C 503
7AC7SOFTWAREPRO D:383 , ASP D:384 , ARG D:471 , HOH D:601 , HOH D:609binding site for residue SO4 D 501
8AC8SOFTWAREPRO B:383 , ASP B:384 , ALA B:385 , ARG B:471 , HOH B:610binding site for residue SO4 B 501
9AC9SOFTWAREARG A:472 , TYR B:310 , VAL B:311 , SER B:312binding site for residue SO4 B 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MHK)

(-) 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:186
                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh..ee.................eee......eee....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mhk A 300 GAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAAVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSFITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLARENAAL 485
                                   309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479      


Chain B from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh....................eee......eee....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mhk B 287 QPRRVELDADATSGAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAAVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSFITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLARENAAL 485
                                   296       306       316       326       336       346       356       366       376       386       396       406       416|      428       438       448       458       468       478       
                                                                                                                                                           416|                                                                  
                                                                                                                                                            419                                                                  


Chain C from PDB  Type:PROTEIN  Length:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh....................eee......eee....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.....hhhhhhhh...hhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mhk C 292 ELDADATSGAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAAVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSFITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLARENAALT 486
                                   301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481     


Chain D from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhh....................eee......eee....hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh....hhhhhhhh.eehhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mhk D 289 RRVELDADATSGAFYARYRDGYVSGEPWPGAGPPPPGRVLYGGLGDSRPGLWGAPEAEEARRRFEASGAPAAVWAPELGDAAQQYALITRLLYTPDAEAMGWLQNPRVVPGDVALDQACFRISGAARNSSSFITGSVARAVPHLGYAMAAGRFGWGLAHAAAAVAMSRRYDRAQKGFLLTSLRRAYAPLLARENAAL 485
                                   298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       


Chain E from PDB  Type:DNA  Length:15
                                               
                 5mhk E  25 CGTGTGGACGATCGG  39
                                    34     


Chain F from PDB  Type:DNA  Length:16
                                                
                 5mhk F   1 CCGATCGTCCACACGG  16
                                    10      


Chain G from PDB  Type:DNA  Length:19
                                                   
                 5mhk G  21 GCTCCGTGTGGACGATCGG  39
                                    30         


Chain H from PDB  Type:DNA  Length:18
                                                  
                 5mhk H   1 CCGATCGTCCACACGGAG  18
                                    10        


Chain J from PDB  Type:PROTEIN  Length:2
                                  
               SCOP domains -- SCOP domains
               CATH domains -- CATH domains
               Pfam domains -- Pfam domains
         Sec.struct. author .. Sec.struct. author
                 SAPs(SNPs) -- SAPs(SNPs)
                    PROSITE -- PROSITE
                 Transcript -- Transcript
                 5mhk J 283 FT 284
   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 5MHK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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