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Conserved domains on  [gi|157864112|ref|XP_001680770|]
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histone H4 [Leishmania major strain Friedlin]

Protein Classification

histone H4( domain architecture ID 11487839)

histone H4 is one of the four histones, along with H2A, H2B and H3, that form the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation

CATH:  1.10.20.10
Gene Ontology:  GO:0006334|GO:0006355|GO:0006325|GO:0046982|GO:0003677
PubMed:  32556547

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00015 PTZ00015
histone H4; Provisional
 1-99 3.19e-46

histone H4; Provisional


:

Pssm-ID: 185397  Cd Length: 102  Bit Score: 143.73  E-value: 3.19e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157864112   1 MAKGKRSADAKSSQKRQKKVLRDNIRGITRGCVRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTV 80
Cdd:PTZ00015   4 MGKGKKSLGAKGGQKRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTV 83

                         90
                 ....*....|....*....
gi 157864112  81 TACDVVNALRQKGHILYGY 99
Cdd:PTZ00015  84 TAMDVVYALKRQGRTLYGF 102
 
Name Accession Description Interval E-value
PTZ00015 PTZ00015
histone H4; Provisional
 1-99 3.19e-46

histone H4; Provisional


Pssm-ID: 185397  Cd Length: 102  Bit Score: 143.73  E-value: 3.19e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157864112   1 MAKGKRSADAKSSQKRQKKVLRDNIRGITRGCVRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTV 80
Cdd:PTZ00015   4 MGKGKKSLGAKGGQKRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTV 83

                         90
                 ....*....|....*....
gi 157864112  81 TACDVVNALRQKGHILYGY 99
Cdd:PTZ00015  84 TAMDVVYALKRQGRTLYGF 102
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 20-98 1.01e-30

histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467037 [Multi-domain]  Cd Length: 79  Bit Score: 103.84  E-value: 1.01e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157864112  20 VLRDNIRGITRGCVRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTVTACDVVNALRQKGHILYG 98
Cdd:cd22912    1 VLRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79
H4 smart00417
Histone H4;
15-88 3.34e-29

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 99.92  E-value: 3.34e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157864112    15 KRQKKVLRDNIRGITRGCVRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTVTACDVVNA 88
Cdd:smart00417   1 RRHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
33-91 1.96e-04

Archaeal histone H3/H4 [Chromatin structure and dynamics];


Pssm-ID: 441639  Cd Length: 67  Bit Score: 36.35  E-value: 1.96e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 157864112  33 VRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTVTACDVVNALRQ 91
Cdd:COG2036    7 VDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
 
Name Accession Description Interval E-value
PTZ00015 PTZ00015
histone H4; Provisional
 1-99 3.19e-46

histone H4; Provisional


Pssm-ID: 185397  Cd Length: 102  Bit Score: 143.73  E-value: 3.19e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157864112   1 MAKGKRSADAKSSQKRQKKVLRDNIRGITRGCVRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTV 80
Cdd:PTZ00015   4 MGKGKKSLGAKGGQKRQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTV 83

                         90
                 ....*....|....*....
gi 157864112  81 TACDVVNALRQKGHILYGY 99
Cdd:PTZ00015  84 TAMDVVYALKRQGRTLYGF 102
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 20-98 1.01e-30

histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component of the nucleosome, which wraps and compacts DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication, and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called the histone code, and nucleosome remodeling. The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.


Pssm-ID: 467037 [Multi-domain]  Cd Length: 79  Bit Score: 103.84  E-value: 1.01e-30
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 157864112  20 VLRDNIRGITRGCVRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTVTACDVVNALRQKGHILYG 98
Cdd:cd22912    1 VLRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79
H4 smart00417
Histone H4;
15-88 3.34e-29

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 99.92  E-value: 3.34e-29
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 157864112    15 KRQKKVLRDNIRGITRGCVRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTVTACDVVNA 88
Cdd:smart00417   1 RRHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74
PLN00035 PLN00035
histone H4; Provisional
 11-99 5.83e-28

histone H4; Provisional


Pssm-ID: 177669 [Multi-domain]  Cd Length: 103  Bit Score: 97.60  E-value: 5.83e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157864112  11 KSSQKRQKKVLRDNIRGITRGCVRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTVTACDVVNALR 90
Cdd:PLN00035  13 KGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALK 92


                 ....*....
gi 157864112  91 QKGHILYGY 99
Cdd:PLN00035  93 RQGRTLYGF 101
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 28-90 9.31e-07

histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally conserved interaction motif involved in heterodimerization of the core histones and their assembly into the nucleosome octamer. Histone fold heterodimers play crucial roles in gene regulation. The minimal HFD consists of three alpha helices connected by two short, unstructured loops. The HFD is found in core histones, TATA box-binding protein-associated factors (TAFs), and many other transcription factors. HFD plays a role in the nucleosomal core particle by conserving histone interactions; these contain more than one HFD. The structure of the nucleosome core particle has two modes that have the largest interaction surfaces, and these are the H3-H4 and H2A-H2B heterodimer interactions. Several TAFs interact via histone-fold (HF) motifs. Five HF-containing TAF pairs have been described in transcription factor II D (TFIID): TAF6-TAF9, TAF4-TAF12, TAF11-TAF13, TAF8-TAF10 and TAF3-TAF10.


Pssm-ID: 467021  Cd Length: 63  Bit Score: 42.20  E-value: 9.31e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157864112  28 ITRGCVRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTVTACDVVNALR 90
Cdd:cd00076    1 LLRSAVARILKSAGFDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
PLN00163 PLN00163
histone H4; Provisional
 15-57 4.97e-05

histone H4; Provisional


Pssm-ID: 165730  Cd Length: 59  Bit Score: 37.75  E-value: 4.97e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 157864112  15 KRQKKVLRDNIRGITRGCVRRMARRGGVKRISSEVYGEVRRVL 57
Cdd:PLN00163  17 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRTVL 59
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 33-90 6.30e-05

histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription regulators and similar proteins; The family includes many archaeal histone-fold proteins and histone-like transcription regulators, which may bind and compact DNA (95 to 150 base pairs) to form nucleosome-like structures that contain positive DNA supercoils. They can increase the resistance of DNA to thermal denaturation.


Pssm-ID: 467034  Cd Length: 64  Bit Score: 37.52  E-value: 6.30e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 157864112  33 VRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTVTACDVVNALR 90
Cdd:cd22909    7 VKRIIKKAGAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
33-91 1.96e-04

Archaeal histone H3/H4 [Chromatin structure and dynamics];


Pssm-ID: 441639  Cd Length: 67  Bit Score: 36.35  E-value: 1.96e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 157864112  33 VRRMARRGGVKRISSEVYGEVRRVLKAYLEDIVRCSTAYTEYARKKTVTACDVVNALRQ 91
Cdd:COG2036    7 VDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
HFD_TAF8 cd22918
histone-fold domain found in transcription initiation factor TFIID subunit 8 (TAF8) and ...
 57-94 7.54e-03

histone-fold domain found in transcription initiation factor TFIID subunit 8 (TAF8) and similar proteins; TAF8, also called TATA Binding Protein (TBP) associated factor 8, protein taube nuss, TBP-associated factor 43 kDa, TBP-associated factor 8, or transcription initiation factor TFIID 43 kDa subunit (TAFII-43, TAFII43), is a component of the TFIID complex that is composed of TATA binding protein (TBP) and a number of TBP-associated factors (TAFs). TFIID is one of the general transcription factors required for accurate and regulated initiation by RNA polymerase II. It plays a central role in mediating promoter responses to various activators and repressors. TAF8 mediates both basal and activator-dependent transcription. It is involved in the differentiation of preadipocyte fibroblasts to adipocytes, however, it does not seem to play a role in differentiation of myoblasts. TAF8 is required for the integration of TAF10 in the TAF complex. It may be important for survival of cells of the inner cell mass which constitute the pluripotent cell population of the early embryo.


Pssm-ID: 467043  Cd Length: 84  Bit Score: 32.52  E-value: 7.54e-03
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 157864112  57 LKAYLEDIVRCSTAYTEYARKKTVTACDVVNALRQKGH 94
Cdd:cd22918   34 LQSYLTEIGRSSKAYCELAGRTEPTLSDVVLALIDMGI 71
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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