Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE ISOLATED HISTONE H2A-H2B HETERODIMER
 
Authors :  Y. Moriwaki, T. Yamane, H. Ohtomo, M. Ikeguchi, J. Kurita, M. Sato, A. Na H. Shimojo, Y. Nishimura
Date :  28 Mar 16  (Deposition) - 25 May 16  (Release) - 25 May 16  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  C,D  (10x)
NMR Structure *:  C,D  (1x)
Keywords :  Nucleosome, Histone, H2A, H2B, Dna Binding Protein, Cs-Rosetta, Nuclear Protein-Nuclear Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Moriwaki, T. Yamane, H. Ohtomo, M. Ikeguchi, J. Kurita, M. Sato, A. Nagadoi, H. Shimojo, Y. Nishimura
Solution Structure Of The Isolated Histone H2A-H2B Heterodimer
Sci Rep V. 6 24999 2016
PubMed-ID: 27181506  |  Reference-DOI: 10.1038/SREP24999

(-) Compounds

Molecule 1 - HISTONE H2A TYPE 1-B/E
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET-23B
    Gene: HIST1H2AB, H2AFM, HIST1H2AE, H2AFA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H2A.2, HISTONE H2A/A, HISTONE H2A/M
 
Molecule 2 - HISTONE H2B TYPE 1-J
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector: PET-23B
    Gene: HIST1H2BJ, H2BFR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HISTONE H2B.1, HISTONE H2B.R, H2B/R

 Structural Features

(-) Chains, Units

  12
NMR Structure (10x): CD
NMR Structure * (1x): CD

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2RVQ)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RVQ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RVQ)

(-) Sequences/Alignments

NMR Structure
   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 C from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............................hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhh................................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rvq C  -3 GPGMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKKTESHHKAKGK 129
                                     6        16        26        36        46        56        66        76        86        96       106       116       126   


Chain D from PDB  Type:PROTEIN  Length:129
                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........................................hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rvq D  -3 GPGMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK 125
                                     6        16        26        36        46        56        66        76        86        96       106       116
   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 2RVQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 23)

NMR Structure(hide GO term definitions)

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2rvq)
 
  Sites
(no "Sites" information available for 2rvq)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2rvq)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2rvq
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  H2A1B_HUMAN | P04908
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  H2B1J_HUMAN | P06899
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  H2A1B_HUMAN | P04908
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  H2B1J_HUMAN | P06899
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        H2A1B_HUMAN | P04908: 2cv5 3a6n 3afa 3an2 3av1 3av2 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3w96 3w97 3w98 3w99 3wkj 3wtp 3x1s 3x1v 4ym5 4ym6 4z5t 5av5 5av6 5av8 5av9 5avb 5avc 5ay8 5b0y 5b0z 5b24 5b2i 5b2j 5b31 5b32 5b40 5cpi 5cpj 5cpk 5gse 5gtc 5gxq 5jrg 5vey 5x7x
        H2B1J_HUMAN | P06899: 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 5fug 5gse 5gtc 5gxq 5jrg 5vey 5x7x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2RVQ)