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(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNLIGANDED E2 DNA BINDING DOMAIN FROM HPV6A
 
Authors :  E. Hooley, R. L. Brady, K. Gaston
Date :  07 Sep 05  (Deposition) - 22 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  A (1x),B (1x),C (1x),D (1x),E (1x),F (1x)
Keywords :  Beta Barrel, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Hooley, V. Fairweather, A. R. Clarke, K. Gaston, R. L. Brady
The Recognition Of Local Dna Conformation By The Human Papillomavirus Type 6 E2 Protein.
Nucleic Acids Res. V. 34 3897 2006
PubMed-ID: 16914454  |  Reference-DOI: 10.1093/NAR/GKL466

(-) Compounds

Molecule 1 - REGULATORY PROTEIN E2
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK-223-3
    Expression System Strain: XL1-BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C TERMINAL DOMAIN
    Gene: E2
    Organism Scientific: HUMAN PAPILLOMAVIRUS TYPE 6A
    Organism Taxid: 37122

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric Unit (2, 17)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2SO412Ligand/IonSULFATE ION
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO45Ligand/IonSULFATE ION
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 4 (2, 7)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SO44Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS D:297 , ARG D:300 , SER D:315 , THR D:316BINDING SITE FOR RESIDUE SO4 D 201
02AC2SOFTWARELYS A:297 , ARG A:300 , SER A:315 , THR A:316BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWARELYS E:297 , ARG E:300 , SER E:315 , THR E:316BINDING SITE FOR RESIDUE SO4 E 203
04AC4SOFTWAREHOH B:64 , ARG B:302 , HIS B:306 , LYS B:349BINDING SITE FOR RESIDUE SO4 B 204
05AC5SOFTWAREHOH D:95 , ARG D:302 , HIS D:306 , LYS D:349BINDING SITE FOR RESIDUE SO4 D 205
06AC6SOFTWAREARG A:302 , LYS A:305 , PRO E:352BINDING SITE FOR RESIDUE SO4 A 206
07AC7SOFTWARELYS F:297 , ARG F:300 , SER F:315 , THR F:316BINDING SITE FOR RESIDUE SO4 F 207
08AC8SOFTWARELYS C:297 , ARG C:300 , SER C:315 , THR C:316BINDING SITE FOR RESIDUE SO4 C 208
09AC9SOFTWAREGLN B:343 , ASN B:346 , HOH C:135 , ARG C:307 , LYS D:323BINDING SITE FOR RESIDUE SO4 C 209
10BC1SOFTWAREHOH A:38 , HOH A:48 , ARG A:302 , HIS A:306 , VAL A:348 , LYS A:349BINDING SITE FOR RESIDUE SO4 A 210
11BC2SOFTWAREHOH C:72 , ARG C:302 , HIS C:306 , LYS C:349BINDING SITE FOR RESIDUE SO4 C 211
12BC3SOFTWAREARG F:302 , HIS F:306 , LYS F:349BINDING SITE FOR RESIDUE SO4 F 212
13BC4SOFTWAREHOH B:33 , HIS B:336 , ALA C:283 , PRO C:285 , HIS C:336 , SER C:337 , GLU C:338BINDING SITE FOR RESIDUE GOL B 367
14BC5SOFTWAREALA E:324 , HOH F:12 , THR F:284 , ASP F:311 , MET F:363 , LEU F:366BINDING SITE FOR RESIDUE GOL F 367
15BC6SOFTWAREHOH A:70 , MET A:361 , HOH B:52 , ILE B:286 , GLN B:288 , THR B:332 , MET B:361BINDING SITE FOR RESIDUE GOL B 368
16BC7SOFTWAREILE C:286 , MET C:361 , HOH D:54 , HOH D:71 , HOH D:130 , ILE D:286 , GLN D:288 , TRP D:317 , THR D:332 , MET D:361BINDING SITE FOR RESIDUE GOL D 367
17BC8SOFTWAREHIS A:318 , HOH B:91 , LYS B:297 , SER B:315 , THR B:316BINDING SITE FOR RESIDUE GOL B 369

(-) SS Bonds  (6, 6)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser C:321 -Pro C:322
2Ala D:324 -Pro D:325

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2AYE)

(-) Exons   (0, 0)

(no "Exon" information available for 2AYE)

(-) 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:86
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:86
                                   292       302       312       322       332       342       352       362      
           VE2_HPV6A    283 SATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d2ayea_ A: Papillomavirus-1 E2 protein                                                 SCOP domains
               CATH domains 2ayeA00 A:282-366  [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
                2aye A  282 SATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   291       301   |   310       320       330       340       350       360      
                                                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 d2ayeb_ B: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 2ayeB00 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
                2aye B  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319       329       339       349       359       
                                                 304A                                                              


Chain C 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 d2ayec_ C: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 2ayeC00 C: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
                2aye C  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319       329       339       349       359       
                                                 304A                                                              


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 d2ayed_ D: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 2ayeD00 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
                2aye 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 d2ayee_ E: Papillomavirus-1 E2 protein                                                  SCOP domains
               CATH domains 2ayeE00 E:281-366  [code=3.30.70.330, no name defined]                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhhhhhh..................eeeeee..hhhhhhhhhhhh.....eeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                2aye E  281 SSATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   290       300    |  309       319       329       339       349       359       
                                                 304A                                                              


Chain F from PDB  Type:PROTEIN  Length:86
 aligned with VE2_HPV6A | Q84294 from UniProtKB/Swiss-Prot  Length:368

    Alignment length:86
                                   292       302       312       322       332       342       352       362      
           VE2_HPV6A    283 SATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSLHLL  368
               SCOP domains d2ayef_ F: Papillomavirus-1 E2 protein                                                 SCOP domains
               CATH domains 2ayeF00 F:282-366  [code=3.30.70.330, no name defined]                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeehhhhhhhhhhhhhhhhhhhh...................eeeee..hhhhhhhhhhhh.....eeeeeeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                2aye F  282 SATPIVQFQGESNCLKCFRYRLNDKHRHLFDLISSTWHWASPKAPHKHAIVTVTYHSEEQRQQFLNVVKIPPTIRHKLGFMSMHLL  366
                                   291       301   |   310       320       330       340       350       360      
                                                304A
   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  (0, 0)

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

(-) 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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  2aye
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  VE2_HPV6A | Q84294
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 Related Entries

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

UniProtKB/Swiss-Prot
        VE2_HPV6A | Q84294: 1r8h 2ayb 2ayg

(-) Related Entries Specified in the PDB File

1r8h SAME PROTEIN, DIFFERENT SPACE GROUP AND ASYMETRIC UNIT
2ayb
2ayg