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(-) Description

Title :  CRYSTAL STRUCTURE OF A HUMAN YL1-H2A.Z-H2B COMPLEX
 
Authors :  C. M. Latrick, M. Marek, K. Ouararhni, C. Papin, I. Stoll, M. Ignatyeva, E. Ennifar, S. Dimitrov, C. Romier, A. Hamiche
Date :  27 Jan 16  (Deposition) - 09 Mar 16  (Release) - 20 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  G,H,I  (1x)
Biol. Unit 2:  D,E,F  (1x)
Biol. Unit 3:  A,B,C  (1x)
Biol. Unit 4:  J,K,L  (1x)
Keywords :  Dna Binding Protein, Histone, Chaperone, Remodeler, H2A. Z, Yl1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Latrick, M. Marek, K. Ouararhni, C. Papin, I. Stoll, M. Ignatyeva A. Obri, E. Ennifar, S. Dimitrov, C. Romier, A. Hamiche
Molecular Basis And Specificity Of H2A. Z-H2B Recognition And Deposition By The Histone Chaperone Yl1
Nat. Struct. Mol. Biol. V. 23 309 2016
PubMed-ID: 26974126  |  Reference-DOI: 10.1038/NSMB.3189

(-) Compounds

Molecule 1 - HISTONE H2A.Z
    Chains: A, D, G, J
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCS
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-MCN
    Fragment: GLOBULAR DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: H2A/Z, HISTONE VARIANT H2A.Z
 
Molecule 2 - VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 72 HOMOLOG
    Chains: C, F, I, L
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCS
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-MCN
    Fragment: N-TERMINAL DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN YL-1, TRANSCRIPTION FACTOR-LIKE 1, HISTONE CHAPERON E YL1
 
Molecule 3 - HISTONE H2B TYPE 1-J
    Chains: B, E, H, K
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNEA-TH
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET-MCN
    Fragment: GLOBULAR DOMAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H2B.1, HISTONE H2B.R, H2B/R, HISTONE H2B

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x):       GHI   
Biological Unit 2 (1x):    DEF      
Biological Unit 3 (1x): ABC         
Biological Unit 4 (1x):          JKL

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 5FUG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly F:66 -Asp F:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FUG)

(-) 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:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....hhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 5fug A  18 SRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAG 106
                                    27        37        47        57        67        77        87        97         


Chain B from PDB  Type:PROTEIN  Length:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 5fug B  35 ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA 124
                                    44        54        64        74        84        94       104       114       124


Chain C from PDB  Type:PROTEIN  Length:51
                                                                                   
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh..hhhhhhhhh.............eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 5fug C   9 PRKTAGNRLSGLLEAEDEFYQTTYGGFTEESGDDEYQGTEDEVDSDFDIDE  65
                                    18     || 30        40       |54        64 
                                          24|                   48|            
                                           27                    53            


Chain D from PDB  Type:PROTEIN  Length:84
                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh....hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh........eehhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 5fug D  18 SRSQRAGLQFPVGRIHRHLKSRRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAG 106
                                    27        37 ||     52        62        72        82        92       102    
                                                39|                                                             
                                                 45                                                             


Chain E from PDB  Type:PROTEIN  Length:91
                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 5fug E  33 RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 123
                                    42        52        62        72        82        92       102       112       122 


Chain F from PDB  Type:PROTEIN  Length:59
                                                                                           
               SCOP domains ----------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhh......................eeee......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 5fug F   9 PRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEYQGDQSDTEDEVDSDFDIDEGD  67
                                    18        28        38        48        58         


Chain G from PDB  Type:PROTEIN  Length:82
                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh....hhhhhhhhhhhh.eehhhhhhhhhhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 5fug G  18 SRSQRAGLQFPVGRIHRHLKSRGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKAT 103
                                    27        37 ||     51        61        71        81        91       101  
                                                39|                                                           
                                                 44                                                           


Chain H from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 5fug H  35 ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 123
                                    44        54        64        74        84        94       104       114         


Chain I from PDB  Type:PROTEIN  Length:54
                                                                                      
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhh..hhhhhhhhh...............eee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                 5fug I   9 PRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEYQGDTEDEVDSDFDIDE  65
                                    18        28        38        48|       61    
                                                                  48|             
                                                                   52             


Chain J from PDB  Type:PROTEIN  Length:85
                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh...hhhhhhhhhhh......eehhhhhhhhhhhhhhhhhhhhhhhh.........eehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------- Transcript
                 5fug J  18 SRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKA 102
                                    27        37        47        57        67        77        87        97     


Chain K from PDB  Type:PROTEIN  Length:89
                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------- Transcript
                 5fug K  35 ESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 123
                                    44        54        64        74        84        94       104       114         


Chain L from PDB  Type:PROTEIN  Length:57
                                                                                         
               SCOP domains --------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhh..hhhhhhhhhh...................eee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------- Transcript
                 5fug L   9 PRKTAGNRLSGLLEAEEEDEFYQTTYGGFTEESGDDEYQGDQSDTEDEVDSDFDIDE  65
                                    18        28        38        48        58
   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 5FUG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 43)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly F:66 - Asp F:67   [ RasMol ]  
 
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  5fug
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  H2AZ_HUMAN | P0C0S5
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  H2B1J_HUMAN | P06899
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    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
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  VPS72_HUMAN | Q15906
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 Related Entries

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

UniProtKB/Swiss-Prot
        H2AZ_HUMAN | P0C0S5: 1f66 3wa9 4cay 4nft 5b31 5b32 5b33 5chl
        H2B1J_HUMAN | P06899: 2rvq 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3w96 3w97 3w98 3w99 3wa9 3waa 3wtp 4cay 4ym5 4ym6 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b33 5b40 5cpi 5cpj 5cpk 5gse 5gtc 5gxq 5jrg 5vey 5x7x

(-) Related Entries Specified in the PDB File

5fue CRYSTAL STRUCTURE OF SCHISTOSOMA MANSONI HDAC8 COMPLEXED WITH 3-BENZAMIDO-BENZOHYDROXAMATE