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(-) Description

Title :  STRUCTURE OF THE EPSTEIN-BARR VIRUS ONCOGENE BARF1
 
Authors :  N. Tarbouriech, F. Ruggiero, M. Deturenne-Tessier, T. Ooka, W. P. Bur
Date :  13 Mar 06  (Deposition) - 31 May 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (3x)
Biol. Unit 2:  B,C  (3x)
Keywords :  Viral Protein, Barf1, Immunoglobulin Domain, Oncogene, Early Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Tarbouriech, F. Ruggiero, M. Deturenne-Tessier, T. Ooka, W. P. Burmeister
Structure Of The Epstein-Barr Virus Oncogene Barf1
J. Mol. Biol. V. 359 667 2006
PubMed-ID: 16647084  |  Reference-DOI: 10.1016/J.JMB.2006.03.056

(-) Compounds

Molecule 1 - 33 KDA EARLY PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HELA
    Expression System Taxid: 9606
    Expression System Vector: ADENOVIRUS
    Organism Scientific: EPSTEIN-BARR VIRUS
    Organism Taxid: 10376
    Strain: B95-8
    Synonym: BARF1, P33

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (3x): A  D
Biological Unit 2 (3x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
1MAN4Ligand/IonALPHA-D-MANNOSE
2NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PT12Ligand/IonPLATINUM (II) ION
Biological Unit 1 (2, 18)
No.NameCountTypeFull Name
1MAN6Ligand/IonALPHA-D-MANNOSE
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PT-1Ligand/IonPLATINUM (II) ION
Biological Unit 2 (2, 18)
No.NameCountTypeFull Name
1MAN6Ligand/IonALPHA-D-MANNOSE
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PT-1Ligand/IonPLATINUM (II) ION

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE A:77 , ASN A:95 , SER A:97 , HIS A:98 , NAG A:1224 , HOH A:2124 , HOH A:2125 , HOH A:2127BINDING SITE FOR RESIDUE NAG A1223
02AC2SOFTWAREPRO A:73 , PHE A:74 , NAG A:1223 , MAN A:1225BINDING SITE FOR RESIDUE NAG A1224
03AC3SOFTWARENAG A:1224BINDING SITE FOR RESIDUE MAN A1225
04AC4SOFTWAREPHE B:77 , ASN B:95 , SER B:97 , HIS B:98 , NAG B:1224 , HOH B:2067 , HOH B:2130BINDING SITE FOR RESIDUE NAG B1223
05AC5SOFTWAREPRO B:73 , PHE B:74 , NAG B:1223 , MAN B:1225BINDING SITE FOR RESIDUE NAG B1224
06AC6SOFTWARENAG B:1224BINDING SITE FOR RESIDUE MAN B1225
07AC7SOFTWAREPHE C:77 , ASN C:95 , SER C:97 , HIS C:98 , NAG C:1225 , HOH C:2076 , HOH C:2142 , HOH C:2143 , HOH C:2144BINDING SITE FOR RESIDUE NAG C1224
08AC8SOFTWAREPRO C:73 , PHE C:74 , NAG C:1224 , MAN C:1226 , HOH C:2144BINDING SITE FOR RESIDUE NAG C1225
09AC9SOFTWARENAG C:1225BINDING SITE FOR RESIDUE MAN C1226
10BC1SOFTWAREPHE D:77 , ASN D:95 , SER D:97 , HIS D:98 , NAG D:1224 , HOH D:2124 , HOH D:2125 , HOH D:2127BINDING SITE FOR RESIDUE NAG D1223
11BC2SOFTWAREPRO D:73 , PHE D:74 , NAG D:1223 , MAN D:1225 , HOH D:2128BINDING SITE FOR RESIDUE NAG D1224
12BC3SOFTWARENAG D:1224BINDING SITE FOR RESIDUE MAN D1225
13BC4SOFTWAREMET A:176 , GLU A:178BINDING SITE FOR RESIDUE PT A1220
14BC5SOFTWAREMET A:160 , HIS A:196 , HOH A:2113BINDING SITE FOR RESIDUE PT A1221
15BC6SOFTWAREARG A:82BINDING SITE FOR RESIDUE PT A1222
16BC7SOFTWAREMET B:176 , GLU B:178BINDING SITE FOR RESIDUE PT B1221
17BC8SOFTWAREMET B:160 , HIS B:196BINDING SITE FOR RESIDUE PT B1222
18BC9SOFTWAREVAL B:38BINDING SITE FOR RESIDUE PT B1226
19CC1SOFTWAREMET C:176 , GLU C:178BINDING SITE FOR RESIDUE PT C1221
20CC2SOFTWAREMET C:160 , HIS C:196 , HOH C:2132BINDING SITE FOR RESIDUE PT C1222
21CC3SOFTWAREMET D:176 , GLU D:178BINDING SITE FOR RESIDUE PT D1220
22CC4SOFTWAREMET D:160 , HIS D:196BINDING SITE FOR RESIDUE PT D1221
23CC5SOFTWAREVAL D:21 , HIS D:118 , SER D:120 , HOH D:2001BINDING SITE FOR RESIDUE PT D1222

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:146 -A:201
2B:146 -B:201
3C:146 -C:201
4D:146 -D:201

(-) Cis Peptide Bonds  (21, 21)

Asymmetric Unit
No.Residues
1Pro A:53 -Gly A:54
2Phe A:136 -Pro A:137
3Phe A:151 -Pro A:152
4Lys A:193 -Pro A:194
5Trp B:35 -Arg B:36
6Arg B:36 -Arg B:37
7Phe B:136 -Pro B:137
8Phe B:151 -Pro B:152
9Lys B:193 -Pro B:194
10Leu B:197 -Pro B:198
11Pro C:53 -Gly C:54
12Phe C:136 -Pro C:137
13Phe C:151 -Pro C:152
14Lys C:193 -Pro C:194
15Leu C:197 -Pro C:198
16Arg D:36 -Arg D:37
17Pro D:53 -Gly D:54
18Phe D:136 -Pro D:137
19Phe D:151 -Pro D:152
20Lys D:193 -Pro D:194
21Leu D:197 -Pro D:198

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2CH8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2CH8)

(-) Exons   (0, 0)

(no "Exon" information available for 2CH8)

(-) 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:188
 aligned with BARF1_EBVB9 | P03228 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:199
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
          BARF1_EBVB9    21 VTAFLGERVTLTSYWRRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRSANTFFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVVKPLTLSVHSERSQFPDFSVLTVTCTVNAFPHPHVQWLMPEGVEPAPTAANGGVMKEKDGSLSVAVDLSLPKPWHLPVTCVGKNDKEEAHGVYVSGYL 219
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeee.....hhhhheeeeeee.....eeeeeeee..eeee.hhh...eeeeee..eeeeee...hhhhheeeeeeeee..eeeeeeeeeeeeeeeeeeeeeee........eeeeeeeeee..eeeeee..-----------...ee.....eeeeeeeee.......eeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ch8 A  21 VTAFLGERVTLTSYWRRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRSANTFFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVVKPLTLSVHSERSQFPDFSVLTVTCTVNAFPHPHVQWLMP-----------GGVMKEKDGSLSVAVDLSLPKPWHLPVTCVGKNDKEEAHGVYVSGYL 219
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160|        -  |    180       190       200       210         
                                                                                                                                                                      161         173                                              


Chain B from PDB  Type:PROTEIN  Length:186
 aligned with BARF1_EBVB9 | P03228 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:200
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
          BARF1_EBVB9    21 VTAFLGERVTLTSYWRRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRSANTFFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVVKPLTLSVHSERSQFPDFSVLTVTCTVNAFPHPHVQWLMPEGVEPAPTAANGGVMKEKDGSLSVAVDLSLPKPWHLPVTCVGKNDKEEAHGVYVSGYLS 220
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeee.....hhhhheeeeeee.....eeeeeeee..eeee.hhhh..eeeeee..eeeeee...hhhhheeeeeeeee..eeeeeeeeeeeeeeeeeeeeeee........eeeeeeeeee..eeeeee.--------------.ee.....eeeeeeeee.......eeeeeee..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ch8 B  21 VTAFLGERVTLTSYWRRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRSANTFFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVVKPLTLSVHSERSQFPDFSVLTVTCTVNAFPHPHVQWLM--------------VMKEKDGSLSVAVDLSLPKPWHLPVTCVGKNDKEEAHGVYVSGYLS 220
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160         -    |  180       190       200       210       220
                                                                                                                                                                     160            175                                             


Chain C from PDB  Type:PROTEIN  Length:186
 aligned with BARF1_EBVB9 | P03228 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:200
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220
          BARF1_EBVB9    21 VTAFLGERVTLTSYWRRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRSANTFFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVVKPLTLSVHSERSQFPDFSVLTVTCTVNAFPHPHVQWLMPEGVEPAPTAANGGVMKEKDGSLSVAVDLSLPKPWHLPVTCVGKNDKEEAHGVYVSGYLS 220
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.....................................hhh...eeeeee..eeeeee...hhhhh......................................................eeeeee.--------------........................eeeeeee..eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ch8 C  21 VTAFLGERVTLTSYWRRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRSANTFFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVVKPLTLSVHSERSQFPDFSVLTVTCTVNAFPHPHVQWLM--------------VMKEKDGSLSVAVDLSLPKPWHLPVTCVGKNDKEEAHGVYVSGYLS 220
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160         -    |  180       190       200       210       220
                                                                                                                                                                     160            175                                             


Chain D from PDB  Type:PROTEIN  Length:186
 aligned with BARF1_EBVB9 | P03228 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:199
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
          BARF1_EBVB9    21 VTAFLGERVTLTSYWRRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRSANTFFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVVKPLTLSVHSERSQFPDFSVLTVTCTVNAFPHPHVQWLMPEGVEPAPTAANGGVMKEKDGSLSVAVDLSLPKPWHLPVTCVGKNDKEEAHGVYVSGYL 219
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.....hhhhh...........................hhh...eeeeee..eeeeee...hhhhh......................................................eeeeee..-------------........................eeeeeee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ch8 D  21 VTAFLGERVTLTSYWRRVSLGPEIEVSWFKLGPGEEQVLIGRMHHDVIFIEWPFRGFFDIHRSANTFFLVVTAANISHDGNYLCRMKLGETEVTKQEHLSVVKPLTLSVHSERSQFPDFSVLTVTCTVNAFPHPHVQWLMP-------------VMKEKDGSLSVAVDLSLPKPWHLPVTCVGKNDKEEAHGVYVSGYL 219
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160|        -    |  180       190       200       210         
                                                                                                                                                                      161           175
   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  (0, 0)

(no "SCOP Domain" information available for 2CH8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2CH8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2CH8)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (BARF1_EBVB9 | P03228)
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  2ch8
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 Related Entries

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        BARF1_EBVB9 | P03228: 3uez 4adf 4adq

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