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(-) Description

Title :  KSHV LANA (ORF73) C-TERMINAL DOMAIN, OPEN NON-RING CONFORMATION: ORTHORHOMBIC CRYSTAL FORM
 
Authors :  R. Ponnusamy, C. E. Mcvey
Date :  02 Jul 15  (Deposition) - 28 Oct 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.80
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  E,F  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Dna Binding Protein, Dna, Viral, Protein Folding, Protein Structure, Tertiary, Rhadinovirus, Viral Proteins, Virus Latency (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Ponnusamy, M. V. Petoukhov, B. Correia, T. F. Custodio, F. Juillard M. Tan, M. Pires De Miranda, M. A. Carrondo, J. P. Simas, K. M. Kaye, D. I. Svergun, C. E. Mcvey
Kshv But Not Mhv-68 Lana Induces A Strong Bend Upon Binding To Terminal Repeat Viral Dna.
Nucleic Acids Res. V. 43 10039 2015
PubMed-ID: 26424851  |  Reference-DOI: 10.1093/NAR/GKV987

(-) Compounds

Molecule 1 - ORF 73
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR PRARE2
    Expression System Vector: PET49B
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN, UNP RESIDUES 1018-1150
    Organism Scientific: HUMAN HERPESVIRUS 8
    Organism Taxid: 37296

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x):     EF  
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x): AB      
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:1123 , ASN A:1131BINDING SITE FOR RESIDUE MG A2146
2AC2SOFTWAREGLU C:1123BINDING SITE FOR RESIDUE MG C2146
3AC3SOFTWAREGLU E:1123 , ASN E:1131BINDING SITE FOR RESIDUE MG E2146
4AC4SOFTWAREGLU G:1123 , ASN G:1131BINDING SITE FOR RESIDUE MG G2146

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A76)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A76)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A76)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A76)

(-) Exons   (0, 0)

(no "Exon" information available for 5A76)

(-) 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:109
                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh....eeeeeeeee..hhhhhhhhhhh.....eeeeeee......eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                5a76 A 1029 AKARPQHIFYRRFLGKDGRPKCQWKFAVIFWGNDPYGLKKLSQAFQFGGVKAGPVSCLPHPITYCVYVYCQNKDTSKKVQMARLAWEASHPLAGNLQSSIVKFKKPLPL 1145
                                  1038      1050      1060      1070      1080      1090|     1106      1116      1126      1136         
                                           1047|                                    1090|                                                
                                            1050                                     1097                                                


Chain B from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhhhhh....eee...ee........eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                5a76 B 1028 PAKARPQHIFYRRFLGKDGRRCQWKFAVIFWGNDPYGLKKLSQAFQFGGVKAGPVSCLPHQSPITYCVYVYCQNKDTSKKVQMARLAWEASHPLAGNLQSSIVKFKKPLPLTQ 1147
                                  1037      1047||    1060      1070      1080      1090|     1104      1114      1124      1134      1144   
                                             1048|                                  1090|                                                    
                                              1052                                   1095                                                    


Chain C from PDB  Type:PROTEIN  Length:114
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......eeeeeeeee.hhhhhhhhhhhh.....eeeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                5a76 C 1029 AKARPQHIFYRRFLGKDGRRDPKCQWKFAVIFWGNDPYGLKKLSQAFQFGGVKAGPVSCLPHDQSPITYCVYVYCQNKDTSKKVQMARLAWEASHPLAGNLQSSIVKFKKPLPL 1145
                                  1038      1048      1058      1068      1078      1088 ||   1101      1111      1121      1131      1141    
                                                                                      1090|                                                   
                                                                                       1094                                                   


Chain D from PDB  Type:PROTEIN  Length:113
                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....eeeeeeeee.hhhhhhhhhhhh.....eeeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                5a76 D 1028 PAKARPQHIFYRRFLGKDGRRDPQWKFAVIFWGNDPYGLKKLSQAFQFGGVKAGPVSCLPHPGPPITYCVYVYCQNKDTSKKVQMARLAWEASHPLAGNLQSSIVKFKKPLPL 1145
                                  1037      1047  ||  1059      1069      1079      1089   || 1102      1112      1122      1132      1142   
                                               1050|                                    1093|                                                
                                                1053                                     1097                                                


Chain E from PDB  Type:PROTEIN  Length:116
                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......eeeeeeeee.hhhhhhhhhhhh....eeeeeeeee.......eeeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                5a76 E 1029 AKARPQHIFYRRFLGKDGRRDPKCQWKFAVIFWGNDPYGLKKLSQAFQFGGVKAGPVSCLPHPGPPITYCVYVYCQNKDTSKKVQMARLAWEASHPLAGNLQSSIVKFKKPLPLTQ 1147
                                  1038      1048      1058      1068      1078      1088    ||1101      1111      1121      1131      1141      
                                                                                         1093|                                                  
                                                                                          1097                                                  


Chain F from PDB  Type:PROTEIN  Length:118
                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh......eeeeeeeee.hhhhhhhhhhhh....eeeeeeee............eeeeeee.hhhhhhhhhhhhhhhhhhh......eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                5a76 F 1029 AKARPQHIFYRRFLGKDGRRDPKCQWKFAVIFWGNDPYGLKKLSQAFQFGGVKAGPVSCLPHPGPDQSPITYCVYVYCQNKDTSKKVQMARLAWEASHPLAGNLQSSIVKFKKPLPLT 1146
                                  1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138        


Chain G from PDB  Type:PROTEIN  Length:116
                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh................hhhhhhhhhhhh.....ee...ee...........eeeeeee.hhhhhhhhhhhhhhhhhhh................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                5a76 G 1029 AKARPQHIFYRRFLGKDGRRDPKCQWKFAVIFWGNDPYGLKKLSQAFQFGGVKAGPVSCLPHPGPDSPITYCVYVYCQNKDTSKKVQMARLAWEASHPLAGNLQSSIVKFKKPLPL 1145
                                  1038      1048      1058      1068      1078      1088     |1099      1109      1119      1129      1139      
                                                                                          1094|                                                 
                                                                                           1096                                                 


Chain H from PDB  Type:PROTEIN  Length:114
                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh................hhhhhhhhhhhh....eee...ee........eeeeeee.hhhhhhhhhhhhhhhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                5a76 H 1029 AKARPQHIFYRRFLGKDGRRDPKCQWKFAVIFWGNDPYGLKKLSQAFQFGGVKAGPVSCLPHQSPITYCVYVYCQNKDTSKKVQMARLAWEASHPLAGNLQSSIVKFKKPLPLT 1146
                                  1038      1048      1058      1068      1078      1088 ||   1102      1112      1122      1132      1142    
                                                                                      1090|                                                   
                                                                                       1095
   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 5A76)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A76)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A76)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5A76)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q76SB0_HHV8 | Q76SB0: 4uzb 4uzc
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        Q76SB0_HHV8 | Q76SB0: 2ypy 2ypz 2yq0

(-) Related Entries Specified in the PDB File

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