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(-) Description

Title :  COMPARISON OF THE STRUCTURE AND DNA BINDING PROPERTIES OF THE E2 PROTEINS FROM AN ONCOGENIC AND A NON-ONCOGENIC HUMAN PAPILLOMAVIRUS
 
Authors :  G. Dell, K. W. Wilkinson, R. Tranter, J. Parish, R. L. Brady, K. Gaston
Date :  24 Oct 03  (Deposition) - 23 Dec 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,E  (1x)
Biol. Unit 3:  C,F  (1x)
Biol. Unit 4:  A,B,C,D,E,F  (1x)
Biol. Unit 5:  A,B  (1x)
Biol. Unit 6:  E,F  (1x)
Biol. Unit 7:  C,D  (1x)
Keywords :  Anti-Parallel Beta-Barrel, Dna-Binding Domain, Transcription, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Dell, K. W. Wilkinson, R. Tranter, J. Parish, R. Leo Brady, K. Gaston
Comparison Of The Structure And Dna-Binding Properties Of The E2 Proteins From An Oncogenic And A Non-Oncogenic Human Papillomavirus.
J. Mol. Biol. V. 334 979 2003
PubMed-ID: 14643661  |  Reference-DOI: 10.1016/J.JMB.2003.10.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN E2
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK223-3
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DNA-BINDING DOMAIN
    Gene: E2
    Organism Scientific: HUMAN PAPILLOMAVIRUS TYPE 6A
    Organism Taxid: 37122

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A  D  
Biological Unit 2 (1x):  B  E 
Biological Unit 3 (1x):   C  F
Biological Unit 4 (1x): ABCDEF
Biological Unit 5 (1x): AB    
Biological Unit 6 (1x):     EF
Biological Unit 7 (1x):   CD  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 14)

Asymmetric Unit (1, 14)
No.NameCountTypeFull Name
1PO414Ligand/IonPHOSPHATE ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1PO45Ligand/IonPHOSPHATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1PO45Ligand/IonPHOSPHATE ION
Biological Unit 3 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 4 (1, 14)
No.NameCountTypeFull Name
1PO414Ligand/IonPHOSPHATE ION
Biological Unit 5 (1, 4)
No.NameCountTypeFull Name
1PO44Ligand/IonPHOSPHATE ION
Biological Unit 6 (1, 5)
No.NameCountTypeFull Name
1PO45Ligand/IonPHOSPHATE ION
Biological Unit 7 (1, 5)
No.NameCountTypeFull Name
1PO45Ligand/IonPHOSPHATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS D:318 , SER D:321 , LYS D:327BINDING SITE FOR RESIDUE PO4 D 501
02AC2SOFTWAREHIS E:318 , ALA E:320 , SER E:321 , LYS E:327 , HOH E:570BINDING SITE FOR RESIDUE PO4 E 502
03AC3SOFTWAREARG D:302 , HIS D:306 , LYS D:349 , HOH D:528 , HOH D:531BINDING SITE FOR RESIDUE PO4 D 503
04AC4SOFTWARESER D:315 , THR D:316 , HOH D:544BINDING SITE FOR RESIDUE PO4 D 504
05AC5SOFTWAREARG E:302 , HIS E:306 , LYS E:349 , HOH E:549 , HOH E:567BINDING SITE FOR RESIDUE PO4 E 505
06AC6SOFTWARELYS E:297 , ARG E:300 , SER E:315 , THR E:316 , HOH E:545BINDING SITE FOR RESIDUE PO4 E 506
07AC7SOFTWARELYS F:297 , ARG F:300 , SER F:315 , THR F:316 , HOH F:541BINDING SITE FOR RESIDUE PO4 F 507
08AC8SOFTWAREARG A:302 , HIS A:306 , LYS A:349 , HOH A:569BINDING SITE FOR RESIDUE PO4 A 508
09AC9SOFTWARELYS B:297 , ARG B:300 , SER B:315 , THR B:316 , HOH B:541BINDING SITE FOR RESIDUE PO4 B 509
10BC1SOFTWAREARG A:300 , SER A:315 , THR A:316 , HOH A:563BINDING SITE FOR RESIDUE PO4 A 510
11BC2SOFTWAREARG B:302 , HIS B:306 , LYS B:349BINDING SITE FOR RESIDUE PO4 B 511
12BC3SOFTWARELYS C:297 , ARG C:300 , SER C:315 , THR C:316 , HOH C:551BINDING SITE FOR RESIDUE PO4 C 512
13BC4SOFTWAREARG F:302 , HIS F:306 , LYS F:349 , HOH F:537BINDING SITE FOR RESIDUE PO4 F 513
14BC5SOFTWAREARG C:302 , LYS C:305 , HIS C:306 , LYS C:349BINDING SITE FOR RESIDUE PO4 C 514

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:295 -D:298
2A:298 -D:295
3B:295 -E:298
4B:298 -E:295
5C:295 -F:298
6C:298 -F:295

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R8H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R8H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R8H)

(-) Exons   (0, 0)

(no "Exon" information available for 1R8H)

(-) 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:87
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:87
                                   291       301       311       321       331       341       351       361       
           VE2_HPV6A    282 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d1r8ha_ A: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 1r8hA00 A:281-366  [code=3.30.70.330, no name defined]                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhhhhh..................eeeeee..hhhhhhhhhhhh......eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                1r8h A  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319       329       339       349       359       
                                                 304A                                                              


Chain B from PDB  Type:PROTEIN  Length:87
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:87
                                   291       301       311       321       331       341       351       361       
           VE2_HPV6A    282 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d1r8hb_ B: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 1r8hB00 B:281-366  [code=3.30.70.330, no name defined]                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhhhhh..................eeeeee..hhhhhhhhhhhh......eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                1r8h B  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319       329       339       349       359       
                                                 304A                                                              


Chain C from PDB  Type:PROTEIN  Length:83
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:87
                                   291       301       311       321       331       341       351       361       
           VE2_HPV6A    282 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d1r8hc_ C: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 1r8hC00 C:281-366  [code=3.30.70.330, no na    me defined]                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhhhhh............----..eeeeee..hhhhhhhhhhhh......eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                1r8h C  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASP----KHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319  |    329       339       349       359       
                                                 304A               322  327                                       


Chain D from PDB  Type:PROTEIN  Length:87
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:87
                                   291       301       311       321       331       341       351       361       
           VE2_HPV6A    282 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d1r8hd_ D: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 1r8hD00 D:281-366  [code=3.30.70.330, no name defined]                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhhhhh..................eeeeee..hhhhhhhhhhhh......eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                1r8h D  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319       329       339       349       359       
                                                 304A                                                              


Chain E from PDB  Type:PROTEIN  Length:87
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:87
                                   291       301       311       321       331       341       351       361       
           VE2_HPV6A    282 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d1r8he_ E: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 1r8hE00 E:281-366  [code=3.30.70.330, no name defined]                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhhhhh..................eeeeee..hhhhhhhhhhhh......eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                1r8h E  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319       329       339       349       359       
                                                 304A                                                              


Chain F from PDB  Type:PROTEIN  Length:83
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:87
                                   291       301       311       321       331       341       351       361       
           VE2_HPV6A    282 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d1r8hf_ F: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 1r8hF00 F:281-366  [code=3.30.70.330, no na    me defined]                              CATH domains
           Pfam domains (1) ----PPV_E2_C-1r8hF01 F:285-362                                                     ---- Pfam domains (1)
           Pfam domains (2) ----PPV_E2_C-1r8hF02 F:285-362                                                     ---- Pfam domains (2)
           Pfam domains (3) ----PPV_E2_C-1r8hF03 F:285-362                                                     ---- Pfam domains (3)
           Pfam domains (4) ----PPV_E2_C-1r8hF04 F:285-362                                                     ---- Pfam domains (4)
           Pfam domains (5) ----PPV_E2_C-1r8hF05 F:285-362                                                     ---- Pfam domains (5)
           Pfam domains (6) ----PPV_E2_C-1r8hF06 F:285-362                                                     ---- Pfam domains (6)
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhhhhh............----..eeeeee..hhhhhhhhhhhh......eeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                1r8h F  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASP----KHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319  |    329       339       349       359       
                                                 304A               322  327
   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, 6)

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

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: no clan defined [family: PPV_E2_C] (7)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (VE2_HPV6A | Q84294)
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: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: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

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

UniProtKB/Swiss-Prot
        VE2_HPV6A | Q84294: 2ayb 2aye 2ayg

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1R8H)