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(-) Description

Title :  CRYSTAL STRUCTURE OF EBV TEGUMENT PROTEIN BNRF1 IN COMPLEX WITH HISTONE CHAPERONE DAXX AND HISTONES H3.3-H4
 
Authors :  H. Huang, D. Patel
Date :  08 Jun 16  (Deposition) - 07 Sep 16  (Release) - 07 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Histone Chaperone, Gene Repression, Chaperone - Dna Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Huang, Z. Deng, O. Vladimirova, A. Wiedmer, F. Lu, P. M. Lieberman, D. Patel
Crystal Structure Of Ebv Tegument Protein Bnrf1 In Complex With Histone Chaperone Daxx And Histones H3. 3-H4
Nat Commun V. 7 2016
PubMed: search  |  Reference-DOI: 10.1038/NCOMMS12707

(-) Compounds

Molecule 1 - HISTONE H3.3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)-CODON PLUS
    Expression System Taxid: 469008
    Gene: H3F3A, H3.3A, H3F3, PP781, H3F3B, H3.3B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HISTONE H4
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)-CODON PLUS
    Expression System Taxid: 469008
    Gene: HIST1H4A, H4/A, H4FA, HIST1H4B, H4/I, H4FI, HIST1H4C, H4/G, H4FG, HIST1H4D, H4/B, H4FB, HIST1H4E, H4/J, H4FJ, HIST1H4F, H4/C, H4FC, HIST1H4H, H4/H, H4FH, HIST1H4I, H4/M, H4FM, HIST1H4J, H4/E, H4FE, HIST1H4K, H4/D, H4FD, HIST1H4L, H4/K, H4FK, HIST2H4A, H4/N, H4F2, H4FN, HIST2H4, HIST2H4B, H4/O, H4FO, HIST4H4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - DEATH DOMAIN-ASSOCIATED PROTEIN 6
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)-CODON PLUS
    Expression System Taxid: 469008
    Fragment: RESIDUES 178-389
    Gene: DAXX, BING2, DAP6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DAXX,HDAXX,ETS1-ASSOCIATED PROTEIN 1,EAP1,FAS DEATH DOMAIN- ASSOCIATED PROTEIN
 
Molecule 4 - MAJOR TEGUMENT PROTEIN
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)-CODON PLUS
    Expression System Taxid: 469008
    Fragment: RESIDUES 381-599
    Gene: BNRF1
    Organism Common: HHV-4
    Organism Scientific: EPSTEIN-BARR VIRUS (STRAIN AG876)
    Organism Taxid: 82830
    Strain: AG876
    Synonym: MTP,PROTEIN P140

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 5KDM)

(-) Sites  (0, 0)

(no "Site" information available for 5KDM)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KDM)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Pro D:445 -Pro D:446
2Gly D:447 -Pro D:448

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KDM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KDM)

(-) Exons   (0, 0)

(no "Exon" information available for 5KDM)

(-) Sequences/Alignments

Asymmetric/Biological 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:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5kdm A  37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    46        56        66        76        86        96       106       116       126         


Chain B from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 5kdm B  26 IQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    35        45        55        65        75        85        95       


Chain C from PDB  Type:PROTEIN  Length:205
                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh......................hhhhhhhh...........hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kdm C 182 RGSRRQIQRLEQLLALYVAEIRRLQEKELDLSELDDPDSAYLQEARLKRKLIRLFGRLCELKDCSSLTGRVIEQRIPYRGTRYPEVNRRIERLINKPGPDTFPDYGDVLRAVEKAAARHSLGLPRQQLQLMAQDAFRDVGIRLQERRHLDLIYNFGCHLTDDYRPGVDPALSDPVLARRLRENRSLAMSRLDEVISKYAMLQDKS 386
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     


Chain D from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeee....hhhhhhhhhhhhhhhhhhhhh...............hhhhhhhh.....eeeee....hhhhhh.....hhhhhhhhhhhh......eeeee..........hhhhhhhhhhhhh...eeeeeeee....eeee....................ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5kdm D 383 LDTVRYDYGHYLIMLGPFYAESSWAQAAVQTALELFSALYPAPCISGYARPPGPSAVIEHLGSLVPKGGLLLFLSHLPDDVKDGLGTGPGMQQFVSSYFLNPACSNVFITVRQRGEKINGRTVLQALGRACDMAGCQHYVLGSTVPLGGLNFVNDLASPVSTAEMMDDFSPFFTVEFPPI 581
                                   392       414       424       434       444       454       464       474     ||491       501       511       521       531       541       551       561       571       581
                                           400|                                                                480|                                                                                             
                                            413                                                                 488
   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  (0, 0)

(no "SCOP Domain" information available for 5KDM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KDM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KDM)

(-) Gene Ontology  (87, 115)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
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  Cis Peptide Bonds
    Gly D:447 - Pro D:448   [ RasMol ]  
    Pro D:445 - Pro D:446   [ RasMol ]  
 

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  MTP_EBVA8 | Q1HVJ0
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 Related Entries

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

UniProtKB/Swiss-Prot
        DAXX_HUMAN | Q9UER7: 2kqs 2kzs 2kzu 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga
        H33_HUMAN | P84243: 1pdq 2l43 3ask 3asl 3av2 3jvk 3muk 3mul 3ql9 3qla 3qlc 3wtp 4gne 4gnf 4gng 4gu0 4gur 4gus 4gy5 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4l58 4n4i 4o62 4qq4 4tmp 4u7t 4w5a 5ay8 5b32 5b33 5bnv 5bnx 5dwq 5dx0 5ja4 5jjy 5jlb 5x7x
        H4_HUMAN | P62805: 1kx4 1kx5 1m18 1m19 1m1a 1s32 1zkk 2bqz 2cv5 2ig0 2kwn 2kwo 2lvm 2qqs 2rje 2rny 2rs9 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3cfs 3cfv 3f9w 3f9x 3f9y 3f9z 3ij1 3jpx 3nqj 3nqu 3o36 3qby 3qzs 3qzt 3qzv 3r45 3uvw 3uvx 3uvy 3uw9 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3wtp 3x1s 3x1t 3x1u 3x1v 4gqb 4h9n 4h9o 4h9p 4h9q 4h9r 4h9s 4hga 4m38 4n3w 4n4f 4qut 4quu 4qyd 4u9w 4ym5 4ym6 4yy6 4yyd 4yyg 4yyh 4yyi 4yyj 4yyk 4yym 4yyn 4z2m 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5bnv 5bnx 5bo0 5c3i 5cpi 5cpj 5cpk 5fa5 5ffw 5fwe 5gse 5gsu 5gt0 5gt3 5gtc 5gxq 5ja4 5jrg 5teg 5x7x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5KDM)