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Conserved domains on  [gi|57753413|ref|YP_184795|]
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Histone [Bracoviriform congregatae]

Protein Classification

histone H4( domain architecture ID 19223581)

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
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 75-152 5.55e-42

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: 134.27  E-value: 5.55e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57753413  75 LRDNIQGITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKRQGRKIYG 152
Cdd:cd22912   2 LRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79
 
Name Accession Description Interval E-value
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 75-152 5.55e-42

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: 134.27  E-value: 5.55e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57753413  75 LRDNIQGITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKRQGRKIYG 152
Cdd:cd22912   2 LRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79
PTZ00015 PTZ00015
histone H4; Provisional
 70-153 2.88e-38

histone H4; Provisional


Pssm-ID: 185397  Cd Length: 102  Bit Score: 125.62  E-value: 2.88e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57753413   70 RHRRSLRDNIQGITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKRQGRK 149
Cdd:PTZ00015  19 RQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRT 98


                 ....
gi 57753413  150 IYGF 153
Cdd:PTZ00015  99 LYGF 102
H4 smart00417
Histone H4;
70-142 1.11e-32

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 110.71  E-value: 1.11e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57753413     70 RHRRSLRDNIQGITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYA 142
Cdd:smart00417   2 RHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
86-145 7.28e-05

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 38.66  E-value: 7.28e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 57753413  86 AIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKR 145
Cdd:COG2036   6 PVDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
CENP-T_C pfam15511
Centromere kinetochore component CENP-T histone fold; CENP-T is a family of vertebral ...
 84-150 2.97e-04

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: 38.18  E-value: 2.97e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57753413    84 KPAIRRLA----RRGGVK-RVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKRQgRKI 150
Cdd:pfam15511  10 TAVVKRLAqrfaRTSGSKgKLSKEALAALEQASDWFFEQMGEDLAAYAKHAGRKTIDESDVILLMKRQ-RQI 80
 
Name Accession Description Interval E-value
HFD_H4 cd22912
histone-fold domain found in histone H4 and similar proteins; Histone H4 is a core component ...
 75-152 5.55e-42

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: 134.27  E-value: 5.55e-42
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 57753413  75 LRDNIQGITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKRQGRKIYG 152
Cdd:cd22912   2 LRDNIQGITKPAIRRLARRGGVKRISGDIYEEVRGVLKDFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYG 79
PTZ00015 PTZ00015
histone H4; Provisional
 70-153 2.88e-38

histone H4; Provisional


Pssm-ID: 185397  Cd Length: 102  Bit Score: 125.62  E-value: 2.88e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57753413   70 RHRRSLRDNIQGITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKRQGRK 149
Cdd:PTZ00015  19 RQKKVLRDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRT 98


                 ....
gi 57753413  150 IYGF 153
Cdd:PTZ00015  99 LYGF 102
PLN00035 PLN00035
histone H4; Provisional
 44-155 1.72e-37

histone H4; Provisional


Pssm-ID: 177669 [Multi-domain]  Cd Length: 103  Bit Score: 123.79  E-value: 1.72e-37
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 57753413   44 KGGKGLEKGEKGsvkggkglgkggakRHRRSLRDNIQGITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAF 123
Cdd:PLN00035   6 KGGKGLGKGGAK--------------RHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAV 71

                         90       100       110
                 ....*....|....*....|....*....|..
gi 57753413  124 HYTEHAKRKTVTSMDIVYALKRQGRKIYGFGS 155
Cdd:PLN00035  72 TYTEHARRKTVTAMDVVYALKRQGRTLYGFGG 103
H4 smart00417
Histone H4;
70-142 1.11e-32

Histone H4;


Pssm-ID: 128694  Cd Length: 74  Bit Score: 110.71  E-value: 1.11e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57753413     70 RHRRSLRDNIQGITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYA 142
Cdd:smart00417   2 RHKKVLRDNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 82-144 5.14e-09

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: 49.52  E-value: 5.14e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57753413  82 ITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALK 144
Cdd:cd00076   1 LLRSAVARILKSAGFDSVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
HFD_CENP-T cd22920
histone-fold domain found in centromere protein T (CENP-T) and similar proteins; CENP-T, also ...
 81-147 5.26e-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: 50.63  E-value: 5.26e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 57753413  81 GITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKRQG 147
Cdd:cd22920   2 SLPKSLVKKLFKHFLKRRVSKEALEALEEISEEFFEQLSDDLEAYADHAGRKTINEKDVELLMKRQR 68
PLN00163 PLN00163
histone H4; Provisional
 72-111 2.60e-08

histone H4; Provisional


Pssm-ID: 165730  Cd Length: 59  Bit Score: 47.76  E-value: 2.60e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 57753413   72 RRSLRDNIQGITKPAIRRLARRGGVKRVSGLVYEEIRDVL 111
Cdd:PLN00163  20 RKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRTVL 59
HFD_archaea_histone-like cd22909
histone-fold domain mainly found in archaeal histone-fold proteins, histone-like transcription ...
 82-144 8.28e-07

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: 44.07  E-value: 8.28e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57753413  82 ITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALK 144
Cdd:cd22909   2 LPKAPVKRIIKKAGAERVSEDAAEELAKLLEEIAEEIAEEAVKLAKHAGRKTVKAEDIELAVK 64
TAF smart00803
TATA box binding protein associated factor; TAFs (TATA box binding protein associated factors) ...
 87-144 9.16e-06

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: 41.07  E-value: 9.16e-06
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 57753413     87 IRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALK 144
Cdd:smart00803   8 IKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65
HHT1 COG2036
Archaeal histone H3/H4 [Chromatin structure and dynamics];
86-145 7.28e-05

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


Pssm-ID: 441639  Cd Length: 67  Bit Score: 38.66  E-value: 7.28e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 57753413  86 AIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKR 145
Cdd:COG2036   6 PVDRIIKKAGAERVSEDAVEALAEILEEYAEEIAKEAVELAKHAGRKTVKAEDIELAAKL 65
CENP-T_C pfam15511
Centromere kinetochore component CENP-T histone fold; CENP-T is a family of vertebral ...
 84-150 2.97e-04

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: 38.18  E-value: 2.97e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 57753413    84 KPAIRRLA----RRGGVK-RVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALKRQgRKI 150
Cdd:pfam15511  10 TAVVKRLAqrfaRTSGSKgKLSKEALAALEQASDWFFEQMGEDLAAYAKHAGRKTIDESDVILLMKRQ-RQI 80
TAF pfam02969
TATA box binding protein associated factor (TAF); TAF proteins adopt a histone-like fold.
 82-144 1.86e-03

TATA box binding protein associated factor (TAF); TAF proteins adopt a histone-like fold.


Pssm-ID: 427084  Cd Length: 66  Bit Score: 35.10  E-value: 1.86e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 57753413    82 ITKPAIRRLARRGGVKRVSGLVYEEIRDVLKIFLKTVIHDAFHYTEHAKRKTVTSMDIVYALK 144
Cdd:pfam02969   4 IPQESVKVVAESLGITNLNDEAAALLAEDVEYRLKEIVQEAAKFMRHSKRTKLTVADVDSALR 66
HFD_POLE4-like cd22929
histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; ...
 114-148 1.99e-03

histone-fold domain found in DNA polymerase epsilon subunit 4 (POLE4) and similar proteins; POLE4, also called DNA polymerase II subunit 4, or DNA polymerase epsilon subunit p12, may participate in DNA repair and in chromosomal DNA replication. It is an accessory component of the DNA polymerase epsilon complex that consists of four subunits: the catalytic subunit POLE and the accessory subunits POLE2, POLE3 and POLE4. POLE4 forms a complex with POLE3. The POLE3-POLE4 is a histone chaperone that promotes tetrasome formation and DNA supercoiling in vitro. Interaction with POLE3 is a prerequisite for further binding with POLE and POLE2. In fungi, POLE4 has been named as DNA polymerase epsilon subunit C (DPB3, also known as DNA polymerase II subunit C). It is an accessory component of the DNA polymerase epsilon (DNA polymerase II) that participates in chromosomal DNA replication. DNA polymerase epsilon is a heterotetramer consisting of POL2, DPB2, DPB3 and DPB4. DPB3 is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. This subfamily also includes protein DLS1 (DPB3-like subunit of ISW2 complex 1). It functions as a component of the ISW2 complex, which at least consists of ISW2, ITC1, DLS1 and DPB4, and acts in remodeling the chromatin by catalyzing an ATP-dependent alteration in the structure of nucleosomal DNA. The ISW2 complex is involved in coordinating transcriptional repression and in inheritance of telomeric silencing. It is involved in repression of MAT a-specific genes, INO1, and early meiotic genes during mitotic growth dependent upon transcription factor UME6 and in a parallel pathway to the RPD3-SIN3 histone deacetylase complex. DLS1 is partially required for the ISW2 complex chromatin remodeling activity and is not required for its interaction with chromatin.


Pssm-ID: 467054 [Multi-domain]  Cd Length: 79  Bit Score: 35.18  E-value: 1.99e-03
                        10        20        30
                ....*....|....*....|....*....|....*
gi 57753413 114 FLKTVIHDAFHYTEHAKRKTVTSMDIVYALKRQGR 148
Cdd:cd22929  37 FIQLLAKEAYSVAQQSKRKTLQLKDIDAAIKSDDR 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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