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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CHROMATIN-TETHERING DOMAIN OF HUMAN CYTOMEGALOVIRUS IE1 PROTEIN BOUND TO THE NUCLEOSOME CORE PARTICLE
 
Authors :  Q. Fang, P. Chen, M. Wang, J. Fang, N. Yang, G. Li, R. M. Xu
Date :  08 Oct 15  (Deposition) - 03 Feb 16  (Release) - 03 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.81
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J,K
Keywords :  Ncp, Ie1, Hcmv, Ctd, Protein Binding-Viral Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Q. Fang, P. Chen, M. Wang, J. Fang, N. Yang, G. Li, R. M. Xu
Human Cytomegalovirus Ie1 Protein Alters The Higher-Order Chromatin Structure By Targeting The Acidic Patch Of The Nucleosome
Elife V. 5 2016
PubMed-ID: 26812545  |  Reference-DOI: 10.7554/ELIFE.11911

(-) Compounds

Molecule 1 - DNA (146-MER)
    ChainsI, J
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainDH5A
    Expression System Taxid562
    Organism CommonHUMAM
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
 
Molecule 2 - HISTONE H3.2
    ChainsA, E
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCDFDUET-1
    Expression System StrainBL21(DE3) CODON PLUS RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonAFRICAN CLAWED FROG
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
 
Molecule 3 - HISTONE H4
    ChainsB, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCDFDUET-1
    Expression System StrainBL21(DE3) CODON PLUS RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonAFRICAN CLAWED FROG
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
 
Molecule 4 - HISTONE H2A
    ChainsC, G
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCDFDUET-1
    Expression System StrainBL21(DE3) CODON PLUS RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneHIST1H2AJ, LOC494591
    Organism CommonAFRICAN CLAWED FROG
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
 
Molecule 5 - HISTONE H2B 1.1
    ChainsD, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCDFDUET-1
    Expression System StrainBL21(DE3) CODON PLUS RIL
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonAFRICAN CLAWED FROG
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355
    SynonymH2B1.1
 
Molecule 6 - C-TERMINAL DOMAIN OF REGULATORY PROTEIN IE1
    ChainsK
    EngineeredYES
    Organism CommonHHV-5
    Organism ScientificHUMAN HERPESVIRUS 5 STRAIN TOWNE
    Organism Taxid10363
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234567891011
Asymmetric/Biological Unit ABCDEFGHIJK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH D:320 , HOH I:306 , HOH J:313 , HOH J:314binding site for residue MG I 201
2AC2SOFTWAREASP C:90 , HIS F:18binding site for residue MG C 201
3AC3SOFTWAREGLU D:102 , LYS D:105 , HIS D:106 , HOH D:301 , DC J:199binding site for residue MG D 201
4AC4SOFTWAREVAL D:45 , HOH D:308 , HOH D:310 , ASP E:77 , HOH E:307 , HOH E:310binding site for residue MG E 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E5A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E5A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E5A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E5A)

(-) Exons   (0, 0)

(no "Exon" information available for 5E5A)

(-) 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.......hhhhhhhhhhhhhhh.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 5e5a A  37 KPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    46        56        66        76        86        96       106       116       126         

Chain B from PDB  Type:PROTEIN  Length:79
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 5e5a B  24 DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    33        43        53        63        73        83        93         

Chain C from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...hhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5e5a C  14 AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK 118
                                    23        33        43        53        63        73        83        93       103       113     

Chain D from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 5e5a D  24 KKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA 121
                                    33        43        53        63        73        83        93       103       113        

Chain E from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 5e5a E  38 PHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 135
                                    47        57        67        77        87        97       107       117       127        

Chain F from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhh..eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 5e5a F  17 RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG 102
                                    26        36        46        56        66        76        86        96      

Chain G from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh...hhhhhhhhhhhh....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh..eee.........hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 5e5a G  14 AKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPK 118
                                    23        33        43        53        63        73        83        93       103       113     

Chain H from PDB  Type:PROTEIN  Length:94
                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                 5e5a H  28 KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA 121
                                    37        47        57        67        77        87        97       107       117    

Chain I from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 5e5a I   1 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT 146
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140      

Chain J from PDB  Type:DNA  Length:146
                                                                                                                                                                                  
                 5e5a J 147 ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGCATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTTGGTAGAATCTGCAGGTGGATATTGAT 292
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286      

Chain K from PDB  Type:PROTEIN  Length:14
                                              
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .............. Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                 5e5a K 477 GKSTHPMVTRSKAD 490
                                   486    

   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 5E5A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E5A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E5A)

(-) Gene Ontology  (18, 42)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        H2A1_XENLA | P068971aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2fj7 2nzd 3b6f 3b6g 3c1b 3c1c 3kuy 3kwq 3lja 3mnn 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4j8u 4j8v 4j8w 4j8x 4ld9 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5f99 5g2e 5hq2 5mlu 5nl0
        H2B11_XENLA | P022811aoi 1f66 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2nzd 3b6f 3b6g 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4j8u 4j8v 4j8w 4j8x 4kgc 4kha 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5cp6 5dnm 5dnn 5f99 5g2e 5hq2 5nl0 5x0x 5x0y
        H32_XENLA | P842331f66 1kx3 1kx4 1kx5 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3c1c 3gv6 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5f99 5hq2 5kgf 5mlu 5nl0 5x0x 5x0y
        H4_XENLA | P627991aoi 1kx3 1kx4 1kx5 1m18 1m19 1m1a 1p34 1p3a 1p3b 1p3f 1p3g 1p3i 1p3k 1p3l 1p3m 1p3o 1p3p 1s32 1zbb 1zla 2f8n 2fj7 2hue 2io5 2nzd 3b6f 3b6g 3c1b 3c1c 3kuy 3kwq 3kxb 3lel 3lja 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mnn 3mvd 3o62 3reh 3rei 3rej 3rek 3rel 3tu4 3ut9 3uta 3utb 4eo5 4j8u 4j8v 4j8w 4j8x 4kgc 4ld9 4r8p 4wu8 4wu9 4xuj 4xzq 4ys3 4z66 4zbj 4zux 5bs7 5bsa 5cp6 5dnm 5dnn 5f99 5hq2 5kgf 5mlu 5nl0 5x0x 5x0y
        Q6AZJ8_XENLA | Q6AZJ82nzd 3b6f 3b6g 3kuy 3kwq 3lja 3mnn 3tu4 3ut9 3uta 3utb 4j8v 4j8w 4j8x 4ld9 4xuj 4xzq 4ys3 4z66 5cp6 5dnm 5dnn 5hq2
        VIE1_HCMVT | P031694qru
UniProtKB/TrEMBL
        Q6AZJ8_XENLA | Q6AZJ83kxb 3lel 3lz0 3lz1 3mgp 3mgq 3mgr 3mgs 3mvd 4kgc 4kha 4r8p 5x0x 5x0y

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5E5A)