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Conserved domains on  [gi|157822485|ref|NP_001101884|]
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histone cluster 1 H2B family member D [Rattus norvegicus]

Protein Classification

histone H2B family protein( domain architecture ID 19223400)

histone H2B is one of 4 core histone proteins, H2A, H2B, H3 and H4 to form the nucleosome core particle

CATH:  1.10.20.10
Gene Ontology:  GO:0003677|GO:0005634|GO:0000786|GO:0046982|GO:0044877|GO:0030527

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 30-123 7.13e-61

histone-fold domain found in histone H2B and similar proteins; Histone H2B 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


:

Pssm-ID: 467035  Cd Length: 94  Bit Score: 181.56  E-value: 7.13e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485  30 RKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAK 109
Cdd:cd22910    1 KKKKRKESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAK 80

                         90
                 ....*....|....
gi 157822485 110 HAVSEGTKAVTKYT 123
Cdd:cd22910   81 HAVSEGTKAVTKYT 94
 
Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 30-123 7.13e-61

histone-fold domain found in histone H2B and similar proteins; Histone H2B 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


Pssm-ID: 467035  Cd Length: 94  Bit Score: 181.56  E-value: 7.13e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485  30 RKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAK 109
Cdd:cd22910    1 KKKKRKESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAK 80

                         90
                 ....*....|....
gi 157822485 110 HAVSEGTKAVTKYT 123
Cdd:cd22910   81 HAVSEGTKAVTKYT 94
H2B smart00427
Histone H2B;
28-124 4.06e-53

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 161.92  E-value: 4.06e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485    28 KKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGEL 107
Cdd:smart00427   1 KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGEL 80

                           90
                   ....*....|....*..
gi 157822485   108 AKHAVSEGTKAVTKYTS 124
Cdd:smart00427  81 AKHAVSEGTKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 12-125 1.54e-52

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 161.40  E-value: 1.54e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485  12 KKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT 91
Cdd:PLN00158   3 KTPSKKPAKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVT 82

                         90       100       110
                 ....*....|....*....|....*....|....
gi 157822485  92 SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 125
Cdd:PLN00158  83 SREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
2-102 3.51e-22

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 84.41  E-value: 3.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485    2 PEPTKSVPAPKKGSKKaVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDT----GISSKAMGIMNSFVNDIFERIAGE 77
Cdd:pfam00125  23 QKSSSSSKKKTRRYRP-GTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTktdlRISADAVVALQEAVEDFLVELFEE 101

                          90       100
                  ....*....|....*....|....*
gi 157822485   78 ASRLAHYNKRSTITSREIQTAVRLL 102
Cdd:pfam00125 102 ANLLAIHAKRVTLTPKDIQLARRLR 126
 
Name Accession Description Interval E-value
HFD_H2B cd22910
histone-fold domain found in histone H2B and similar proteins; Histone H2B is a core component ...
 30-123 7.13e-61

histone-fold domain found in histone H2B and similar proteins; Histone H2B 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. Some histone H2B family members have broad antibacterial activity, which may contribute to the formation of the functional antimicrobial barrier of the colonic epithelium, and to the bactericidal activity of amniotic fluid.


Pssm-ID: 467035  Cd Length: 94  Bit Score: 181.56  E-value: 7.13e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485  30 RKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAK 109
Cdd:cd22910    1 KKKKRKESFSIYIYKVLKQVHPDLGISSKAMDIMNSFVNDIFERIATEASRLARYNKRSTLTSRDIQTAVRLLLPGELAK 80

                         90
                 ....*....|....
gi 157822485 110 HAVSEGTKAVTKYT 123
Cdd:cd22910   81 HAVSEGTKAVTKYT 94
H2B smart00427
Histone H2B;
28-124 4.06e-53

Histone H2B;


Pssm-ID: 197718  Cd Length: 97  Bit Score: 161.92  E-value: 4.06e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485    28 KKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGEL 107
Cdd:smart00427   1 KKRVKKRKETYAIYIYKVLKQVHPDTGISSRAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGEL 80

                           90
                   ....*....|....*..
gi 157822485   108 AKHAVSEGTKAVTKYTS 124
Cdd:smart00427  81 AKHAVSEGTKAVTKASS 97
PLN00158 PLN00158
histone H2B; Provisional
 12-125 1.54e-52

histone H2B; Provisional


Pssm-ID: 215081  Cd Length: 116  Bit Score: 161.40  E-value: 1.54e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485  12 KKGSKKAVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTIT 91
Cdd:PLN00158   3 KTPSKKPAKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVT 82

                         90       100       110
                 ....*....|....*....|....*....|....
gi 157822485  92 SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 125
Cdd:PLN00158  83 SREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116
PTZ00463 PTZ00463
histone H2B; Provisional
 15-124 4.21e-39

histone H2B; Provisional


Pssm-ID: 185642  Cd Length: 117  Bit Score: 127.21  E-value: 4.21e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485  15 SKKAVTKAQKKdgKKRKRSRKESYSVYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSRE 94
Cdd:PTZ00463   9 AKKAATGPDGK--KKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSRE 86

                         90       100       110
                 ....*....|....*....|....*....|
gi 157822485  95 IQTAVRLLLPGELAKHAVSEGTKAVTKYTS 124
Cdd:PTZ00463  87 IQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116
Histone pfam00125
Core histone H2A/H2B/H3/H4;
2-102 3.51e-22

Core histone H2A/H2B/H3/H4;


Pssm-ID: 459682 [Multi-domain]  Cd Length: 126  Bit Score: 84.41  E-value: 3.51e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822485    2 PEPTKSVPAPKKGSKKaVTKAQKKDGKKRKRSRKESYSVYVYKVLKQVHPDT----GISSKAMGIMNSFVNDIFERIAGE 77
Cdd:pfam00125  23 QKSSSSSKKKTRRYRP-GTVALKEIRKYQSSTDLLIYKLPFARVVREVVQSTktdlRISADAVVALQEAVEDFLVELFEE 101

                          90       100
                  ....*....|....*....|....*
gi 157822485   78 ASRLAHYNKRSTITSREIQTAVRLL 102
Cdd:pfam00125 102 ANLLAIHAKRVTLTPKDIQLARRLR 126
HFD_SF cd00076
histone fold domain (HFD) superfamily; The histone fold domain (HFD) is a structurally ...
 42-100 4.79e-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: 41.05  E-value: 4.79e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 157822485  42 VYKVLKQVHPDtGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVR 100
Cdd:cd00076    6 VARILKSAGFD-SVSKSALELLSDLLERYLEELARAAKAYAELAGRTTPNAEDVELALE 63
HFD_TAF12 cd07981
histone-fold domain found in transcription initiation factor TFIID subunit 12 (TAF12) and ...
 46-96 2.68e-03

histone-fold domain found in transcription initiation factor TFIID subunit 12 (TAF12) and similar proteins; TAF12, also called TATA Binding Protein (TBP) associated factor 12, transcription initiation factor TFIID 20/15 kDa subunits, TAFII-20/TAFII-15, or TAFII20/TAFII15, is a TBP-associated factor (TAF). TAFs are components of the transcription factor IID (TFIID) complex, PCAF histone acetylase complex, and TBP-free TAFII complex (TFTC). TIIFD is multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. TFIID and PCAF are composed of TATA binding protein (TBP) and several TAFs. TBP is not part of TFTC. TAFs are essential for mediating regulation of RNA polymerase transcription. TAF12 interacts with TAF4 and makes a novel histone-like heterodimer that binds DNA and has a core promoter function of a subset of genes. It is important for RAS-induced transformation properties of human colorectal cancer cells; its levels are increased in the cells harboring the RAS mutation. Also, TAF12 interacts with activating transcription factor 7 (ATF7) and contributes to the hypersensitivity of osteoclast (OCL) precursors to 1,25-dihydroxyvitamin D2 (1,25-(OH)2D3; also known as calcitriol) in Paget's disease (PD), a disorder of the bone remodeling process, in which the body absorbs old bone and forms abnormal new bone.


Pssm-ID: 467025 [Multi-domain]  Cd Length: 74  Bit Score: 34.43  E-value: 2.68e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 157822485  46 LKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQ 96
Cdd:cd07981   13 VREVDPNERLDPDVEELLLQLADDFVDDVVTFACKLAKHRGSDTLEVKDVQ 63
 
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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