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(-) Description

Title :  FITTING OF THE H2A-H2B HISTONES IN THE ELECTRON MICROSCOPY MAP OF THE COMPLEX NUCLEOPLASMIN:H2A-H2B HISTONES (1:5).
 
Authors :  I. Ramos, J. Martin-Benito, R. Finn, L. Bretana, K. Aloria, J. M. Arizme J. Ausio, A. Muga, J. M. Valpuesta, A. Prado
Date :  02 Sep 10  (Deposition) - 03 Nov 10  (Release) - 20 Mar 13  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  19.50
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Nuclear Protein, Chaperone, Chromatin, Nuclear-Chaperone, Histone-Chaperone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Ramos, J. Martin-Benito, R. Finn, L. Bretana, K. Aloria, J. M. Arizmendi, J. Ausio, A. Muga, J. M. Valpuesta, A. Prado
Nucleoplasmin Binds Histone H2A-H2B Dimers Through Its Distal Face.
J. Biol. Chem. V. 285 33771 2010
PubMed-ID: 20696766  |  Reference-DOI: 10.1074/JBC.M110.150664

(-) Compounds

Molecule 1 - HISTONE H2A-IV
    Cell: ERYTHROCYTE
    Chains: A, C, E, G, I
    Fragment: RESIDUES 16-106
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: H2A HISTONE
 
Molecule 2 - HISTONE H2B 5
    Cell: ERYTHROCYTE
    Chains: B, D, F, H, J
    Fragment: RESIDUES 37-126
    Organism Common: CHICKEN
    Organism Scientific: GALLUS GALLUS
    Organism Taxid: 9031
    Synonym: H2B HISTONE, H2B V

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2XQL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 10)

Asymmetric/Biological Unit (2, 10)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HISTONE_H2APS00046 Histone H2A signature.H2A4_CHICK22-28
 
 
 
 		  5A:21-27
C:21-27
E:21-27
G:21-27
I:21-27
2HISTONE_H2BPS00357 Histone H2B signature.H2B5_CHICK93-115
 
 
 
 		  5B:92-114
D:92-114
F:92-114
H:92-114
J:92-114

(-) Exons   (0, 0)

(no "Exon" information available for 2XQL)

(-) 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:91
 aligned with H2A4_CHICK | P02263 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:91
                                    25        35        45        55        65        75        85        95       105 
           H2A4_CHICK    16 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 106
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HISTONE------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2xql A  15 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 105
                                    24        34        44        54        64        74        84        94       104 


Chain B from PDB  Type:PROTEIN  Length:90
 aligned with H2B5_CHICK | P0C1H4 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:90
                                    46        56        66        76        86        96       106       116       126
           H2B5_CHICK    37 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 126
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------HISTONE_H2B            ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2xql B  36 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 125
                                    45        55        65        75        85        95       105       115       125


Chain C from PDB  Type:PROTEIN  Length:91
 aligned with H2A4_CHICK | P02263 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:91
                                    25        35        45        55        65        75        85        95       105 
           H2A4_CHICK    16 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 106
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HISTONE------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2xql C  15 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 105
                                    24        34        44        54        64        74        84        94       104 


Chain D from PDB  Type:PROTEIN  Length:90
 aligned with H2B5_CHICK | P0C1H4 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:90
                                    46        56        66        76        86        96       106       116       126
           H2B5_CHICK    37 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 126
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------HISTONE_H2B            ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2xql D  36 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 125
                                    45        55        65        75        85        95       105       115       125


Chain E from PDB  Type:PROTEIN  Length:91
 aligned with H2A4_CHICK | P02263 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:91
                                    25        35        45        55        65        75        85        95       105 
           H2A4_CHICK    16 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 106
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HISTONE------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2xql E  15 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 105
                                    24        34        44        54        64        74        84        94       104 


Chain F from PDB  Type:PROTEIN  Length:90
 aligned with H2B5_CHICK | P0C1H4 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:90
                                    46        56        66        76        86        96       106       116       126
           H2B5_CHICK    37 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 126
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------HISTONE_H2B            ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2xql F  36 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 125
                                    45        55        65        75        85        95       105       115       125


Chain G from PDB  Type:PROTEIN  Length:91
 aligned with H2A4_CHICK | P02263 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:91
                                    25        35        45        55        65        75        85        95       105 
           H2A4_CHICK    16 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 106
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh....hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HISTONE------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2xql G  15 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 105
                                    24        34        44        54        64        74        84        94       104 


Chain H from PDB  Type:PROTEIN  Length:90
 aligned with H2B5_CHICK | P0C1H4 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:90
                                    46        56        66        76        86        96       106       116       126
           H2B5_CHICK    37 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 126
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------HISTONE_H2B            ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2xql H  36 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 125
                                    45        55        65        75        85        95       105       115       125


Chain I from PDB  Type:PROTEIN  Length:91
 aligned with H2A4_CHICK | P02263 from UniProtKB/Swiss-Prot  Length:129

    Alignment length:91
                                    25        35        45        55        65        75        85        95       105 
           H2A4_CHICK    16 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 106
               SCOP domains ------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Histone-2xqlI01 I:17-90                                                   --------------- Pfam domains (1)
           Pfam domains (2) --Histone-2xqlI02 I:17-90                                                   --------------- Pfam domains (2)
           Pfam domains (3) --Histone-2xqlI03 I:17-90                                                   --------------- Pfam domains (3)
           Pfam domains (4) --Histone-2xqlI04 I:17-90                                                   --------------- Pfam domains (4)
           Pfam domains (5) --Histone-2xqlI05 I:17-90                                                   --------------- Pfam domains (5)
         Sec.struct. author .hhhhhh....hhhhhhhhhhhh....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eehhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------HISTONE------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                 2xql I  15 KSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQG 105
                                    24        34        44        54        64        74        84        94       104 


Chain J from PDB  Type:PROTEIN  Length:90
 aligned with H2B5_CHICK | P0C1H4 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:90
                                    46        56        66        76        86        96       106       116       126
           H2B5_CHICK    37 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 126
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Histone-2xqlJ01 J:36-101                                          ------------------------ Pfam domains (1)
           Pfam domains (2) Histone-2xqlJ02 J:36-101                                          ------------------------ Pfam domains (2)
           Pfam domains (3) Histone-2xqlJ03 J:36-101                                          ------------------------ Pfam domains (3)
           Pfam domains (4) Histone-2xqlJ04 J:36-101                                          ------------------------ Pfam domains (4)
           Pfam domains (5) Histone-2xqlJ05 J:36-101                                          ------------------------ Pfam domains (5)
         Sec.struct. author .hhhhhhhhhhhhh...eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------HISTONE_H2B            ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 2xql J  36 SYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK 125
                                    45        55        65        75        85        95       105       115       125
   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 2XQL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 10)

Asymmetric/Biological Unit
(-)
Clan: Histone (49)

(-) Gene Ontology  (9, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,C,E,G,I   (H2A4_CHICK | P02263)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0006342    chromatin silencing    Repression of transcription by altering the structure of chromatin, e.g. by conversion of large regions of DNA into an inaccessible state often called heterochromatin.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Chain B,D,F,H,J   (H2B5_CHICK | P0C1H4)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
biological process
    GO:0006334    nucleosome assembly    The aggregation, arrangement and bonding together of a nucleosome, the beadlike structural units of eukaryotic chromatin composed of histones and DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000788    nuclear nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA in the nucleus into higher order structures.
    GO:0000786    nucleosome    A complex comprised of DNA wound around a multisubunit core and associated proteins, which forms the primary packing unit of DNA into higher order structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        H2A4_CHICK | P02263: 1eqz 1hio 1hq3 1tzy 2aro 2hio 3c9k
        H2B5_CHICK | P0C1H4: 1eqz 1hio 1hq3 1tzy 2aro 2hio

(-) Related Entries Specified in the PDB File

1eqz X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION RELATED ID: EMD-1777 RELATED DB: EMDB STRUCTURE OF THE COMPLEX NUCLEOPLASMIN:H2A-H2B HISTONES.
1hio HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN, ALPHACARBONS ONLY
1hq3 CRYSTAL STRUCTURE OF THE HISTONE-CORE- OCTAMER INKCL/PHOSPHATE
1tzy CRYSTAL STRUCTURE OF THE CORE-HISTONE OCTAMER TO 1.90ANGSTROM RESOLUTION
2aro CRYSTAL STRUCTURE OF THE NATIVE HISTONE OCTAMER TO 2.1ANGSTROM RESOLUTION, CRYSTALISED IN THE PRESENCE OF S-NITROSOGLUTATHIONE
2hio HISTONE OCTAMER (CHICKEN), CHROMOSOMAL PROTEIN