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.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 4504301   22 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 100
Cdd:cd22912   1 VLRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79

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

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504301   34 AIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKR 93
Cdd:COG2036   6 PVDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65

histone H4; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 4504301    18 RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97
Cdd:PTZ00015  19 RQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRT 98

                 ....
gi 4504301    98 LYGF 101
Cdd:PTZ00015  99 LYGF 102

Histone H4;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4504301      18 RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYA 90
Cdd:smart00417   2 RHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 4504301   29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 95
Cdd:cd22920   2 SLPKSLVKKLFKHFLKRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDVELLMKRQR 68

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.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 4504301   30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALK 92
Cdd:cd00076   1 LLRSAVARILKSAGFDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 4504301      35 IRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALK 92
Cdd:smart00803   8 IKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65

histone-fold domain found in transcription initiation factor TFIID subunit 9 (TAF9) and similar proteins; The family includes TAF9 (also called TATA Binding Protein (TBP) associated factor 9, RNA polymerase II TBP-associated factor subunit G, STAF31/32, transcription initiation factor TFIID 31 kDa subunit, TAFII-31, TAFII31, transcription initiation factor TFIID 32 kDa subunit, TAFII-32, or TAFII32) and TAF9-like (also called transcription initiation factor TFIID subunit 9B, neuronal cell death-related protein 7, DN-7, or transcription-associated factor TAFII31L), which are essential for cell viability. They are involved in transcriptional activation as well as the repression of distinct but overlapping sets of genes. They may have roles in gene regulation associated with apoptosis. Both TAF9 and TAF9-like are TAFs that are components of the transcription factor IID (TFIID) complex, the TBP-free TAFII complex (TFTC), the PCAF histone acetylase complex and the STAGA transcription coactivator-HAT complex. TFIID or TFTC are essential for the regulation of RNA polymerase II-mediated transcription. TAF9 interacts directly with different transcription factors such as p53, herpes simplex virus activator vp16, and the basal transcription factor TFIIB.

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 4504301   34 AIRRLARRGGVKRisgliYEEtrGVLKVFLE-------NVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97
Cdd:cd07979   6 VIRAILKSMGVTD-----YEP--RVVNQLLEfayryttEVLQDAKVYAEHAGRSQIDEEDVRLAIQSRADH 69