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(-) Description

Title :  CRYSTAL STRUCTURE AT 1.7 ANGSTROMS OF THE BOVINE PAPILLOMAVIRUS-1 E2 DNA-BINDING DOMAIN BOUND TO ITS DNA TARGET
 
Authors :  R. S. Hegde, S. R. Grossman, L. A. Laimins, P. B. Sigler
Date :  13 Jan 94  (Deposition) - 31 Jan 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Protein-Dna Complex, Double Helix, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. S. Hegde, S. R. Grossman, L. A. Laimins, P. B. Sigler
Crystal Structure At 1. 7 A Of The Bovine Papillomavirus-1 E2 Dna-Binding Domain Bound To Its Dna Target.
Nature V. 359 505 1992
PubMed-ID: 1328886  |  Reference-DOI: 10.1038/359505A0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA (5'- D(*CP*CP*GP*AP*CP*CP*GP*AP*CP*GP*TP*CP*GP*GP*TP*CP*G )-3')
    Chains: B
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - PROTEIN (E2)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BOVINE PAPILLOMAVIRUS TYPE 1
    Organism Taxid: 10559

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1YB2Ligand/IonYTTERBIUM (III) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1YB-1Ligand/IonYTTERBIUM (III) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:354 , ASP A:365 , ASN A:366 , GLU A:369BINDING SITE FOR RESIDUE YB A 499
2AC2SOFTWAREHOH B:612 , HOH B:613 , HOH B:620BINDING SITE FOR RESIDUE YB B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2BOP)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2BOP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BOP)

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 2BOP)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:85
 aligned with VE2_BPV1 | P03122 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:85
                                   335       345       355       365       375       385       395       405     
             VE2_BPV1   326 SCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF 410
               SCOP domains d2bopa_ A: Papillomavirus-1 E2 protein                                                SCOP domains
               CATH domains 2bopA00 A:326-410  [code=3.30.70.330, no name defined]                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
     Sec.struct. author (1) --------hhhhhhhhhhhhhhhh...eeeeeeeeeeeee...eeeeeeeeeeeeehhhhhhhhhhhh.....eeeeeeeeeeee Sec.struct. author (1)
     Sec.struct. author (2) eeeeeeeee---------------------------------------------------------------------------- Sec.struct. author (2)
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 2bop A 326 SCFALISGTANQVKCYRFRVKKNHRHRYENCTTTWFTVADNGAERQGQAQILITFGSPSQRQDFLKHVPLPPGMNISGFTASLDF 410
                                   335       345       355       365       375       385       395       405     


Chain B from PDB  Type:DNA  Length:17
                                                 
                 2bop B   1 CCGACCGACGTCGGTCG  17
                                    10
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BOP)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (VE2_BPV1 | P03122)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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: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:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0039693    viral DNA genome replication    The replication of a viral DNA genome.
    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.

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 Related Entries

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        VE2_BPV1 | P03122: 1dbd 1jjh 2jeu 2jex

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