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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HPV-18 E2 DNA-BINDING DOMAIN
 
Authors :  S. S. Kim, J. Tam, A. F. Wang, R. Hegde
Date :  10 Jul 00  (Deposition) - 15 Nov 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Dimeric Beta Barrel, Activator, Dna-Binding, Trans-Acting Factor, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. S. Kim, J. K. Tam, A. F. Wang, R. S. Hegde
The Structural Basis Of Dna Target Discrimination By Papillomavirus E2 Proteins.
J. Biol. Chem. V. 275 31245 2000
PubMed-ID: 10906136  |  Reference-DOI: 10.1074/JBC.M004541200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN E2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET3
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 287-365 OF HPV-18 E2 WITH GSHM
    Organism Scientific: HUMAN PAPILLOMAVIRUS TYPE 18
    Organism Taxid: 333761

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH D:17 , HOH D:74 , LYS D:300 , ARG D:303 , SER D:318 , THR D:319BINDING SITE FOR RESIDUE SO4 D 901
2AC2SOFTWARELYS C:300 , ARG C:303 , SER C:318 , THR C:319BINDING SITE FOR RESIDUE SO4 C 902

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F9F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F9F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F9F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F9F)

(-) Exons   (0, 0)

(no "Exon" information available for 1F9F)

(-) 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:76
 aligned with VE2_HPV18 | P06790 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:81
                                   294       304       314       324       334       344       354       364 
            VE2_HPV18   285 NTTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWTGAGNEKTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMTM 365
               SCOP domains d1f9fa_ A: Papillomavirus-1 E2 protein                                            SCOP domains
               CATH domains 1f9fA00 A:285-365  [code=3.30.70.330,      no name defined]                       CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhhhhhhhh....ee......-----..eeeeeee..hhhhhhhhhhhh......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 1f9f A 285 HMTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHW-----EKTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMTM 365
                                   294       304       314       | -   |   334       344       354       364 
                                                               322   328                                     


Chain B from PDB  Type:PROTEIN  Length:77
 aligned with VE2_HPV18 | P06790 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:82
                                   293       303       313       323       333       343       353       363  
            VE2_HPV18   284 GNTTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWTGAGNEKTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMTM 365
               SCOP domains d1f9fb_ B: Papillomavirus-1 E2 protein                                             SCOP domains
               CATH domains 1f9fB00 B:284-365  [code=3.30.70.330, no      name defined]                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeehhhhhhhhhhhh.hhhhh.ee.......-----.eeeeeee..hhhhhhhhhhhh......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1f9f B 284 SHMTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWT-----KTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMTM 365
                                   293       303       313       323     | 333       343       353       363  
                                                                 323   329                                    


Chain C from PDB  Type:PROTEIN  Length:76
 aligned with VE2_HPV18 | P06790 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:82
                                   293       303       313       323       333       343       353       363  
            VE2_HPV18   284 GNTTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWTGAGNEKTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMTM 365
               SCOP domains d1f9fc_ C: Papillomavirus-1 E2 protein                                             SCOP domains
               CATH domains 1f9fC00 C:284-365  [code=3.30.70.330, no       name defined]                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeehhhhhhhhhhhhhhhh....ee.......------.eeeeee..hhhhhhhhhhhh......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1f9f C 284 SHMTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWT------TGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMTM 365
                                   293       303       313       323      |333       343       353       363  
                                                                 323    330                                   


Chain D from PDB  Type:PROTEIN  Length:82
 aligned with VE2_HPV18 | P06790 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:82
                                   293       303       313       323       333       343       353       363  
            VE2_HPV18   284 GNTTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWTGAGNEKTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMTM 365
               SCOP domains d1f9fd_ D: Papillomavirus-1 E2 protein                                             SCOP domains
               CATH domains 1f9fD00 D:284-365  [code=3.30.70.330, no name defined]                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhhhhhhhhh....ee..............eeeeee..hhhhhhhhhhhh......eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1f9f D 284 SHMTPIIHLKGDRNSLKCLRYRLRKHSDHYRDISSTWHWTGAGNEKTGILTVTYHSETQRTKFLNTVAIPDSVQILVGYMTM 365
                                   293       303       313       323       333       343       353       363
   Legend:   → Mismatch (orange background)
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  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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F9F)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (VE2_HPV18 | P06790)
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: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.
    GO:0044163    host cytoskeleton    Any of the various filamentous elements that form the internal framework of host cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the host cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the host cell. The various elements of the host cytoskeleton not only serve in the maintenance of host cellular shape but also have roles in other host cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.

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        VE2_HPV18 | P06790: 1jj4 1qqh 1tue

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