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(-) Description

Title :  EBNA-1 NUCLEAR PROTEIN/DNA COMPLEX
 
Authors :  A. Bochkarev, E. Bochkareva, A. Edwards, L. Frappier
Date :  14 Dec 98  (Deposition) - 15 Dec 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nuclear Protein, Protein-Dna Complex, Dna-Binding, Activator, Origin-Binding Protein, Protein/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Bochkarev, E. Bochkareva, L. Frappier, A. M. Edwards
The 2. 2 A Structure Of A Permanganate-Sensitive Dna Site Bound By The Epstein-Barr Virus Origin Binding Protein, Ebna1.
J. Mol. Biol. V. 284 1273 1998
PubMed-ID: 9878348  |  Reference-DOI: 10.1006/JMBI.1998.2247
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*GP*GP*GP*AP*AP*GP*CP*AP*TP*AP*TP*GP*CP*TP*TP*CP*CP*C)- 3')
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - PROTEIN (NUCLEAR PROTEIN EBNA1)
    Cellular Location: NUCLEAR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)PLUSS
    Expression System Taxid: 562
    Fragment: DNA-BINDING AND DIMERIZATION DOMAIN RESIDUES 459 - 607
    Organism Common: EPSTEIN-BARR VIRUS
    Organism Scientific: HUMAN HERPESVIRUS 4
    Organism Taxid: 10376
    Strain: GD1
    Synonym: EBNA-1 NUCLEAR PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1B3T)

(-) Sites  (0, 0)

(no "Site" information available for 1B3T)

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:598 -B:598

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:588 -Pro A:589
2Ala B:588 -Pro B:589

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1B3T)

(-) Exons   (0, 0)

(no "Exon" information available for 1B3T)

(-) Sequences/Alignments

Asymmetric/Biological 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:147
 aligned with EBNA1_EBVB9 | P03211 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:147
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       
          EBNA1_EBVB9   461 KGGWFGKHRGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP 607
               SCOP domains d1b3ta_ A: Epstein barr virus nuclear antigen-1 (ebna1)                                                                                             SCOP domains
               CATH domains 1b3tA00 A:461-607  [code=3.30.70.390, no name defined]                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhh.............eeeeeee..hhhhhhhhhhhhhh.................................eeeeee..hhhhhhhhhhhhhhhh.....hhheeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b3t A 461 KGGWFGKHRGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP 607
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       


Chain A from PDB  Type:PROTEIN  Length:147
 aligned with Q69477_EBVG | Q69477 from UniProtKB/TrEMBL  Length:203

    Alignment length:147
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       
          Q69477_EBVG    23 KGGWFGKHRGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP 169
               SCOP domains d1b3ta_ A: Epstein barr virus nuclear antigen-1 (ebna1)                                                                                             SCOP domains
               CATH domains 1b3tA00 A:461-607  [code=3.30.70.390, no name defined]                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhh.............eeeeeee..hhhhhhhhhhhhhh.................................eeeeee..hhhhhhhhhhhhhhhh.....hhheeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b3t A 461 KGGWFGKHRGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP 607
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with EBNA1_EBVB9 | P03211 from UniProtKB/Swiss-Prot  Length:641

    Alignment length:147
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       
          EBNA1_EBVB9   461 KGGWFGKHRGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP 607
               SCOP domains d1b3tb_ B: Epstein barr virus nuclear antigen-1 (ebna1)                                                                                             SCOP domains
               CATH domains 1b3tB00 B:461-607  [code=3.30.70.390, no name defined]                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhh.............eeeeeee..hhhhhhhhhhhhhh.................................eeeeee..hhhhhhhhhhhhhhhhh....hhheeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b3t B 461 KGGWFGKHRGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP 607
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       


Chain B from PDB  Type:PROTEIN  Length:147
 aligned with Q69477_EBVG | Q69477 from UniProtKB/TrEMBL  Length:203

    Alignment length:147
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       
          Q69477_EBVG    23 KGGWFGKHRGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP 169
               SCOP domains d1b3tb_ B: Epstein barr virus nuclear antigen-1 (ebna1)                                                                                             SCOP domains
               CATH domains 1b3tB00 B:461-607  [code=3.30.70.390, no name defined]                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhhhhhhhhhhhh.............eeeeeee..hhhhhhhhhhhhhh.................................eeeeee..hhhhhhhhhhhhhhhhh....hhheeeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b3t B 461 KGGWFGKHRGQGGSNPKFENIAEGLRALLARSHVERTTDEGTWVAGVFVYGGSKTSLYNLRRGTALAIPQCRLTPLSRLPFGMAPGPGPQPGPLRESIVCYFMVFLQTHIFAEVLKDAIKDLVMTKPAPTCNIRVTVCSFDDGVDLP 607
                                   470       480       490       500       510       520       530       540       550       560       570       580       590       600       


Chain C from PDB  Type:DNA  Length:18
                                                  
                 1b3t C 101 GGGAAGCATATGCTTCCC 118
                                   110        


Chain D from PDB  Type:DNA  Length:18
                                                  
                 1b3t D 201 GGGAAGCATATGCTTCCC 218
                                   210
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1B3T)

(-) Gene Ontology  (15, 23)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (EBNA1_EBVB9 | P03211)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0030683    evasion or tolerance by virus of host immune response    Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0039644    suppression by virus of host NF-kappaB transcription factor activity    Any process in which a virus stops, prevents, or reduces the activity of host NF-kappaB activity.
    GO:0039504    suppression by virus of host adaptive immune response    Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the adaptive immune response of the host organism, an immune response based on directed amplification of specific receptors for antigen produced through a somatic diversification process, and allowing for enhanced response to subsequent exposures to the same antigen (immunological memory).
    GO:0039588    suppression by virus of host antigen processing and presentation    Any viral process that inhibits a host antigen-presenting cell expressing a peptide antigen on its cell surface in association with an MHC protein complex.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Chain A,B   (Q69477_EBVG | Q69477)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003688    DNA replication origin binding    Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006275    regulation of DNA replication    Any process that modulates the frequency, rate or extent of DNA replication.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
cellular component
    GO:0042025    host cell nucleus    A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

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    Ala A:588 - Pro A:589   [ RasMol ]  
    Ala B:588 - Pro B:589   [ RasMol ]  
 

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  1b3t
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 Related Entries

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

UniProtKB/Swiss-Prot
        EBNA1_EBVB9 | P03211: 1vhi 1yy6 2fyy 2fz3 3mv7 3mv8 3mv9 4pra 4pre 4pri 4prp 5wum 5wun

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1B3T)