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Conserved domains on  [gi|6324298|ref|NP_014368|]
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histone H4 [Saccharomyces cerevisiae S288C]

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
 18-101 1.55e-45

histone H4; Provisional


:

Pssm-ID: 185397  Cd Length: 102  Bit Score: 142.19  E-value: 1.55e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324298    18 RHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRT 97
Cdd:PTZ00015  19 RQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRT 98


                 ....
gi 6324298    98 LYGF 101
Cdd:PTZ00015  99 LYGF 102
 
Name Accession Description Interval E-value
PTZ00015 PTZ00015
histone H4; Provisional
 18-101 1.55e-45

histone H4; Provisional


Pssm-ID: 185397  Cd Length: 102  Bit Score: 142.19  E-value: 1.55e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324298    18 RHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRT 97
Cdd:PTZ00015  19 RQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRT 98


                 ....
gi 6324298    98 LYGF 101
Cdd:PTZ00015  99 LYGF 102
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 22-100 9.14e-45

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: 139.28  E-value: 9.14e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6324298   22 ILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYG 100
Cdd:cd22912   1 VLRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79
H4 smart00417
Histone H4;
18-90 8.97e-35

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 113.79  E-value: 8.97e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324298      18 RHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYA 90
Cdd:smart00417   2 RHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
34-93 3.01e-06

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 41.36  E-value: 3.01e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324298   34 AIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKR 93
Cdd:COG2036   6 PVDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
CENP-T_C pfam15511
Centromere kinetochore component CENP-T histone fold; CENP-T is a family of vertebral ...
 32-97 8.41e-06

Centromere kinetochore component CENP-T histone fold; CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin.


Pssm-ID: 434768  Cd Length: 108  Bit Score: 40.88  E-value: 8.41e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6324298     32 KPAIRRLA-----RRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRT 97
Cdd:pfam15511  10 TAVVKRLAqrfarTSGSKGKLSKEALAALEQASDWFFEQMGEDLAAYAKHAGRKTIDESDVILLMKRQRQI 80
 
Name Accession Description Interval E-value
PTZ00015 PTZ00015
histone H4; Provisional
 18-101 1.55e-45

histone H4; Provisional


Pssm-ID: 185397  Cd Length: 102  Bit Score: 142.19  E-value: 1.55e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324298    18 RHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRT 97
Cdd:PTZ00015  19 RQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRT 98


                 ....
gi 6324298    98 LYGF 101
Cdd:PTZ00015  99 LYGF 102
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 22-100 9.14e-45

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: 139.28  E-value: 9.14e-45
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 6324298   22 ILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRTLYG 100
Cdd:cd22912   1 VLRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79
PLN00035 PLN00035
histone H4; Provisional
 18-103 8.27e-44

histone H4; Provisional


Pssm-ID: 177669 [Multi-domain]  Cd Length: 103  Bit Score: 137.66  E-value: 8.27e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324298    18 RHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRT 97
Cdd:PLN00035  18 RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97


                 ....*.
gi 6324298    98 LYGFGG 103
Cdd:PLN00035  98 LYGFGG 103
H4 smart00417
Histone H4;
18-90 8.97e-35

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 113.79  E-value: 8.97e-35
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324298      18 RHRKILRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYA 90
Cdd:smart00417   2 RHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74
PLN00163 PLN00163
histone H4; Provisional
 23-59 5.63e-11

histone H4; Provisional


Pssm-ID: 165730  Cd Length: 59  Bit Score: 53.15  E-value: 5.63e-11
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 6324298    23 LRDNIQGITKPAIRRLARRGGVKRISGLIYEEVRAVL 59
Cdd:PLN00163  23 LRDNIQGITKPAIRRLARRGGVKRISGLIYEETRTVL 59
HFD_CENP-T cd22920
histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also ...
 29-95 1.47e-09

histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also called interphase centromere complex protein 22 (ICEN22), is a component of the CENPA-NAC (nucleosome-associated) complex, which plays a central role in the assembly of kinetochore proteins, mitotic progression, and chromosome segregation. The CENPA-NAC complex recruits the CENPA-CAD (nucleosome distal) complex and may be involved in incorporation of newly synthesized CENPA into centromeres. CENP-T is also part of a nucleosome-associated complex that binds specifically to histone H3-containing nucleosomes at the centromere, as opposed to nucleosomes containing CENPA. Moreover, CENP-T is a component of the heterotetrameric CENP-T-W-S-X complex that binds and supercoils DNA, and plays an important role in kinetochore assembly. CENP-T has a fundamental role in kinetochore assembly and function. It is one of the inner kinetochore proteins, with most further proteins binding downstream. It is required for normal chromosome organization and normal progress through mitosis.


Pssm-ID: 467045  Cd Length: 94  Bit Score: 50.25  E-value: 1.47e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 6324298   29 GITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQG 95
Cdd:cd22920   2 SLPKSLVKKLFKHFLKRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDVELLMKRQR 68
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 30-92 4.11e-08

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: 46.00  E-value: 4.11e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324298   30 ITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALK 92
Cdd:cd22909   2 LPKAPVKRIIKKAGAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 30-92 1.68e-06

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: 41.82  E-value: 1.68e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 6324298   30 ITKPAIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALK 92
Cdd:cd00076   1 LLRSAVARILKSAGFDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
34-93 3.01e-06

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 41.36  E-value: 3.01e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 6324298   34 AIRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKR 93
Cdd:COG2036   6 PVDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
CENP-T_C pfam15511
Centromere kinetochore component CENP-T histone fold; CENP-T is a family of vertebral ...
 32-97 8.41e-06

Centromere kinetochore component CENP-T histone fold; CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin.


Pssm-ID: 434768  Cd Length: 108  Bit Score: 40.88  E-value: 8.41e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 6324298     32 KPAIRRLA-----RRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALKRQGRT 97
Cdd:pfam15511  10 TAVVKRLAqrfarTSGSKGKLSKEALAALEQASDWFFEQMGEDLAAYAKHAGRKTIDESDVILLMKRQRQI 80
TAF smart00803
TATA box binding protein associated factor; TAFs (TATA box binding protein associated factors) ...
 35-92 5.13e-04

TATA box binding protein associated factor; TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.


Pssm-ID: 129039  Cd Length: 65  Bit Score: 35.29  E-value: 5.13e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 6324298      35 IRRLARRGGVKRISGLIYEEVRAVLKSFLESVIRDSVTYTEHAKRKTVTSLDVVYALK 92
Cdd:smart00803   8 IKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65
 
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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