NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|157819381|ref|NP_001102821|]
View 

H1.8 linker histone [Rattus norvegicus]

Protein Classification

histone H1/H5 family protein( domain architecture ID 10049384)

histone H1/H5 family protein similar to a linker histone (H1 or H5), which is a chromatin-associated protein that binds to the exterior of nucleosomes and dramatically stabilizes the highly condensed states of chromatin fibers

CATH:  1.10.10.10
Gene Ontology:  GO:0006334|GO:0003677|GO:0030527|GO:0000786
PubMed:  26212454|16345076|10973918|11149891
SCOP:  4000178

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 44-135 2.73e-20

linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber


:

Pssm-ID: 238028 [Multi-domain]  Cd Length: 88  Bit Score: 83.82  E-value: 2.73e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157819381  44 GQRNPTMLRMVLEALKAREKRQGTSVVAIKVYIQHKYPTVGtTRFKYLLKQALETGMRRGLLTRPansKAKGATGSFKLV 123
Cdd:cd00073    1 PPSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDD-ENFNKLLKLALKKGVAKGKLVQV---KGTGASGSFKLS 76

                         90
                 ....*....|..
gi 157819381 124 PKPKKKRTCAPK 135
Cdd:cd00073   77 KKKKKKKKPAKK 88
PTZ00121 super family cl31754
MAEBL; Provisional
 127-329 8.55e-03

MAEBL; Provisional


The actual alignment was detected with superfamily member PTZ00121:

Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 38.20  E-value: 8.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157819381  127 KKKRTCAPKARGGATGTKETGSKESGLRKKDQVGKAKTEKAAPNPGRKRKAYPCSAATLEKAPKNAKAVPREVREAPLKR 206
Cdd:PTZ00121 1301 KKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKA 1380

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157819381  207 DKAAGAPLTANIGQKVKHSGTGQEADAHGKTKDVCEKSKASASKVQnsvASLIKKEMAAIAHMETVVQGAKTVQKTKAPT 286
Cdd:PTZ00121 1381 DAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKK---AEEKKKADEAKKKAEEAKKADEAKKKAEEAK 1457

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 157819381  287 PSQDVRHKAQPTTRVRKTKTPEDTKRPQLPPKTSSKAPSKKAE 329
Cdd:PTZ00121 1458 KAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKAD 1500
 
Name Accession Description Interval E-value
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 44-135 2.73e-20

linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber


Pssm-ID: 238028 [Multi-domain]  Cd Length: 88  Bit Score: 83.82  E-value: 2.73e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157819381  44 GQRNPTMLRMVLEALKAREKRQGTSVVAIKVYIQHKYPTVGtTRFKYLLKQALETGMRRGLLTRPansKAKGATGSFKLV 123
Cdd:cd00073    1 PPSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDD-ENFNKLLKLALKKGVAKGKLVQV---KGTGASGSFKLS 76

                         90
                 ....*....|..
gi 157819381 124 PKPKKKRTCAPK 135
Cdd:cd00073   77 KKKKKKKKPAKK 88
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 48-120 4.56e-17

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 74.48  E-value: 4.56e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157819381   48 PTMLRMVLEALKAREKRQGTSVVAIKVYIQHKYPTVGTTRFKYLLKQALETGMRRGLLTRPansKAKGATGSF 120
Cdd:pfam00538   2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGDVAKFNSLLKRALKKGVEKGTLVQP---KGTGASGSF 71
H15 smart00526
Domain in histone families 1 and 5;
48-110 2.63e-07

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 47.19  E-value: 2.63e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157819381    48 PTMLRMVLEALKAREKRQGTSVVAIKVYIQHKYpTVGTTRFKYLLKQALETGMRRGLLTRPAN 110
Cdd:smart00526   5 PPYSEMIVEAISALKERKGSSLQAIKKYIEANY-KVLPNNFRKLLKLALKRLVASGKLVQVKG 66
PTZ00121 PTZ00121
MAEBL; Provisional
 127-329 8.55e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 38.20  E-value: 8.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157819381  127 KKKRTCAPKARGGATGTKETGSKESGLRKKDQVGKAKTEKAAPNPGRKRKAYPCSAATLEKAPKNAKAVPREVREAPLKR 206
Cdd:PTZ00121 1301 KKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKA 1380

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157819381  207 DKAAGAPLTANIGQKVKHSGTGQEADAHGKTKDVCEKSKASASKVQnsvASLIKKEMAAIAHMETVVQGAKTVQKTKAPT 286
Cdd:PTZ00121 1381 DAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKK---AEEKKKADEAKKKAEEAKKADEAKKKAEEAK 1457

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 157819381  287 PSQDVRHKAQPTTRVRKTKTPEDTKRPQLPPKTSSKAPSKKAE 329
Cdd:PTZ00121 1458 KAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKAD 1500
 
Name Accession Description Interval E-value
H15 cd00073
linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, ...
 44-135 2.73e-20

linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber


Pssm-ID: 238028 [Multi-domain]  Cd Length: 88  Bit Score: 83.82  E-value: 2.73e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157819381  44 GQRNPTMLRMVLEALKAREKRQGTSVVAIKVYIQHKYPTVGtTRFKYLLKQALETGMRRGLLTRPansKAKGATGSFKLV 123
Cdd:cd00073    1 PPSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDD-ENFNKLLKLALKKGVAKGKLVQV---KGTGASGSFKLS 76

                         90
                 ....*....|..
gi 157819381 124 PKPKKKRTCAPK 135
Cdd:cd00073   77 KKKKKKKKPAKK 88
Linker_histone pfam00538
linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin ...
 48-120 4.56e-17

linker histone H1 and H5 family; Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures Histone H1 is replaced by histone H5 in some cell types.


Pssm-ID: 459846 [Multi-domain]  Cd Length: 71  Bit Score: 74.48  E-value: 4.56e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157819381   48 PTMLRMVLEALKAREKRQGTSVVAIKVYIQHKYPTVGTTRFKYLLKQALETGMRRGLLTRPansKAKGATGSF 120
Cdd:pfam00538   2 PPYSDMIKEAIKALKERKGSSRQAIKKYIKANYKVGDVAKFNSLLKRALKKGVEKGTLVQP---KGTGASGSF 71
H15 smart00526
Domain in histone families 1 and 5;
48-110 2.63e-07

Domain in histone families 1 and 5;


Pssm-ID: 197772 [Multi-domain]  Cd Length: 66  Bit Score: 47.19  E-value: 2.63e-07
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 157819381    48 PTMLRMVLEALKAREKRQGTSVVAIKVYIQHKYpTVGTTRFKYLLKQALETGMRRGLLTRPAN 110
Cdd:smart00526   5 PPYSEMIVEAISALKERKGSSLQAIKKYIEANY-KVLPNNFRKLLKLALKRLVASGKLVQVKG 66
PTZ00121 PTZ00121
MAEBL; Provisional
 127-329 8.55e-03

MAEBL; Provisional


Pssm-ID: 173412 [Multi-domain]  Cd Length: 2084  Bit Score: 38.20  E-value: 8.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157819381  127 KKKRTCAPKARGGATGTKETGSKESGLRKKDQVGKAKTEKAAPNPGRKRKAYPCSAATLEKAPKNAKAVPREVREAPLKR 206
Cdd:PTZ00121 1301 KKKADEAKKKAEEAKKADEAKKKAEEAKKKADAAKKKAEEAKKAAEAAKAEAEAAADEAEAAEEKAEAAEKKKEEAKKKA 1380

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157819381  207 DKAAGAPLTANIGQKVKHSGTGQEADAHGKTKDVCEKSKASASKVQnsvASLIKKEMAAIAHMETVVQGAKTVQKTKAPT 286
Cdd:PTZ00121 1381 DAAKKKAEEKKKADEAKKKAEEDKKKADELKKAAAAKKKADEAKKK---AEEKKKADEAKKKAEEAKKADEAKKKAEEAK 1457

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 157819381  287 PSQDVRHKAQPTTRVRKTKTPEDTKRPQLPPKTSSKAPSKKAE 329
Cdd:PTZ00121 1458 KAEEAKKKAEEAKKADEAKKKAEEAKKADEAKKKAEEAKKKAD 1500
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH