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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PAPILLOMAVIRUS DNA TETHERING COMPLEX E2:BRD4
 
Authors :  E. A. Abbate, C. Voitenleitner, M. R. Botchan
Date :  24 Oct 06  (Deposition) - 09 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Protein-Peptide Complex, Helical Peptide, Three Helix Bundle, Amphipathic Helix, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. A. Abbate, C. Voitenleitner, M. R. Botchan
Structure Of The Papillomavirus Dna-Tethering Complex E2:Brd4 And A Peptide That Ablates Hpv Chromosomal Association.
Mol. Cell V. 24 877 2006
PubMed-ID: 17189190  |  Reference-DOI: 10.1016/J.MOLCEL.2006.11.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATORY PROTEIN E2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX2T
    Expression System StrainXA90
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentACTIVATION DOMAIN
    GeneE2
    Organism ScientificHUMAN PAPILLOMAVIRUS TYPE 16
    Organism Taxid333760
 
Molecule 2 - BROMODOMAIN-CONTAINING PROTEIN 4
    ChainsB
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX2T
    Expression System StrainXA90
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL RESIDUES (1343-1362)
    GeneBRD4, HUNK1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHUNK1 PROTEIN

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2NNU)

(-) Sites  (0, 0)

(no "Site" information available for 2NNU)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:105 -Pro A:106

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002633771ENSE00001113198chr19:15391262-15391075188BRD4_HUMAN-00--
1.2ENST000002633772ENSE00001113202chr19:15383944-15383626319BRD4_HUMAN1-95950--
1.3ENST000002633773ENSE00000689046chr19:15379853-15379716138BRD4_HUMAN96-141460--
1.4ENST000002633774ENSE00000689047chr19:15378362-15378227136BRD4_HUMAN142-187460--
1.5ENST000002633775ENSE00000689048chr19:15376454-15376165290BRD4_HUMAN187-283970--
1.6ENST000002633776ENSE00000348853chr19:15375577-15375215363BRD4_HUMAN284-4041210--
1.7ENST000002633777ENSE00000689050chr19:15374359-15374231129BRD4_HUMAN405-447430--
1.8ENST000002633778ENSE00000689051chr19:15367984-15367775210BRD4_HUMAN448-517700--
1.9ENST000002633779ENSE00000689052chr19:15367074-15366875200BRD4_HUMAN518-584670--
1.10ENST0000026337710ENSE00000689053chr19:15366403-15366108296BRD4_HUMAN584-6831000--
1.11ENST0000026337711ENSE00001187704chr19:15365073-15364963111BRD4_HUMAN683-720380--
1.15ENST0000026337715ENSE00001113203chr19:15355573-1535552153BRD4_HUMAN720-737180--
1.16ENST0000026337716ENSE00001055985chr19:15355411-15355042370BRD4_HUMAN738-8611240--
1.17ENST0000026337717ENSE00001055976chr19:15354298-15353711588BRD4_HUMAN861-10571970--
1.18ENST0000026337718ENSE00001136676chr19:15350833-15350721113BRD4_HUMAN1057-1094380--
1.19ENST0000026337719ENSE00001113200chr19:15350632-15350470163BRD4_HUMAN1095-1149550--
1.20ENST0000026337720ENSE00001113199chr19:15350333-15350203131BRD4_HUMAN1149-1192440--
1.21ENST0000026337721ENSE00000951121chr19:15350075-15349870206BRD4_HUMAN1193-1261690--
1.22ENST0000026337722ENSE00000951122chr19:15349791-15349554238BRD4_HUMAN1261-1340800--
1.23ENST0000026337723ENSE00001055981chr19:15349256-15348301956BRD4_HUMAN1341-1362221B:1343-136220

(-) 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:201
 aligned with VE2_HPV16 | P03120 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:201
                             1                                                                                                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199 
           VE2_HPV16      - -METLCQRLNVCQDKILTHYENDSTDLRDHIDYWKHMRLECAIYYKAREMGFKHINHQVVPTLAVSKNKALQAIELQLTLETIYNSQYSNEKWTLQDVSLEVYLTAPTGCIKKHGYTVEVQFDGDICNTMHYTNWTHIYICEEASVTVVEGQVDYYGLYYVHEGIRTYFVQFKDDAEKYSKNKVWEVHAGGQVILCPTSVF  200
               SCOP domains d2nnua_ A: E2 regulatory, transactivation domain                                                                                                                                                          SCOP domains
               CATH domains 2nnuA01 A:0-101  [code=1.10.287.30, no name defined]                                                  2nnuA02 A:102-200  [code=2.170.200.10, no name defined]                                             CATH domains
               Pfam domains -PPV_E2_N-2nnuA01 A:1-200                                                                                                                                                                                 Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...ee..ee..hhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhh.....eeeeeeeeeeee......eeeeeeeeeeeeee..eeeee..ee...eeeeee..eeeeeeehhhhhhhhh....eeee....ee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2nnu A    0 SMETLCQRLNVCQDKILTHYENDSTDLRDHIDYWKHMRLECAIYYKAREMGFKHINHQVVPTLAVSKNKALQAIELQLTLETIYNSQYSNEKWTLQDVSLEVYLTAPTGCIKKHGYTVEVQFDGDICNTMHYTNWTHIYICEEASVTVVEGQVDYYGLYYVHEGIRTYFVQFKDDAEKYSKNKVWEVHAGGQVILCPTSVF  200
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199 

Chain B from PDB  Type:PROTEIN  Length:20
 aligned with BRD4_HUMAN | O60885 from UniProtKB/Swiss-Prot  Length:1362

    Alignment length:20
                                  1352      1362
          BRD4_HUMAN   1343 ATIDMNFQSDLLSIFEENLF 1362
               SCOP domains -------------------- SCOP domains
               CATH domains -------------------- CATH domains
               Pfam domains -------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------- SAPs(SNPs)
                    PROSITE -------------------- PROSITE
               Transcript 1 Exon 1.23            Transcript 1
                2nnu B 1343 ATIDMNFQSDLLSIFEENLF 1362
                                  1352      1362

   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, 1)

Asymmetric Unit

(-) CATH Domains  (2, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (29, 42)

Asymmetric Unit(hide GO term definitions)
Chain A   (VE2_HPV16 | P03120)
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.

Chain B   (BRD4_HUMAN | O60885)
molecular function
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0070577    lysine-acetylated histone binding    Interacting selectively and non-covalently with a histone in which a lysine residue has been modified by acetylation.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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).
biological process
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:2000002    negative regulation of DNA damage checkpoint    Any process that stops, prevents, or reduces the frequency, rate or extent of a DNA damage checkpoint.
    GO:0010971    positive regulation of G2/M transition of mitotic cell cycle    Any process that increases the rate or extent of progression from G2 phase to M phase of the mitotic cell cycle.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0032968    positive regulation of transcription elongation from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription elongation, the extension of an RNA molecule after transcription initiation and promoter clearance by the addition of ribonucleotides, catalyzed by RNA polymerase II.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:1901407    regulation of phosphorylation of RNA polymerase II C-terminal domain    Any process that modulates the frequency, rate or extent of phosphorylation of RNA polymerase II C-terminal domain.
    GO:0000083    regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
    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:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        BRD4_HUMAN | O608852i8n 2lsp 2mjv 2n3k 2ncz 2nd0 2nd1 2oss 2ouo 2yel 2yem 3mxf 3p5o 3svf 3svg 3u5j 3u5k 3u5l 3uvw 3uvx 3uvy 3uw9 3zyu 4a9l 4bjx 4bw1 4bw2 4bw3 4bw4 4c66 4c67 4cfk 4cfl 4cl9 4clb 4don 4e96 4f3i 4gpj 4hbv 4hbw 4hbx 4hby 4hxk 4hxl 4hxm 4hxn 4hxo 4hxp 4hxr 4hxs 4ioo 4ioq 4ior 4j0r 4j0s 4j3i 4kv1 4kv4 4lr6 4lrg 4lyi 4lys 4lyw 4lzr 4lzs 4men 4meo 4mep 4meq 4mr3 4mr4 4nqm 4nr8 4nuc 4nud 4nue 4o70 4o71 4o72 4o74 4o75 4o76 4o77 4o78 4o7a 4o7b 4o7c 4o7e 4o7f 4ogi 4ogj 4pce 4pci 4ps5 4qb3 4qr3 4qr4 4qr5 4qzs 4uix 4uiy 4uiz 4uyd 4whw 4wiv 4x2i 4xy9 4xya 4yh3 4yh4 4z1q 4z1s 4z93 4zc9 4zw1 5a5s 5a85 5acy 5ad2 5ad3 5bt4 5cfw 5coi 5cp5 5cpe 5cqt 5crm 5crz 5cs8 5ctl 5cy9 5d0c 5d24 5d25 5d26 5d3h 5d3j 5d3l 5d3n 5d3p 5d3r 5d3s 5d3t 5dlx 5dlz 5dw2 5dx4 5e0r 5egu 5ei4 5eis 5f5z 5f60 5f61 5f62 5f63 5fbx 5h21 5hcl 5hls 5hm0 5hq5 5hq6 5hq7 5i80 5i88 5igk 5jwm 5khm 5ku3 5lj1 5lj2 5luu 5t35 5u28 5u2c 5u2e 5u2f 5ueo 5uep 5ueq 5uer 5ues 5uet 5ueu 5uev 5uex 5uey 5uez 5uf0 5ula 5uoo 5uvs 5uvt 5uvu 5uvv 5uvw 5uvx 5uvy 5uvz 5wuu
        VE2_HPV16 | P031201by9 1dto 1r8p 1zzf 2q79 3mi7

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