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Conserved domains on  [gi|157874106|pdb|1DZ1|B]
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Chain B, Mouse HP1 (M31) C terminal (shadow chromo) domain

Protein Classification

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
CSD_HP1beta_Cbx1 cd18654
chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 ...
11-68 1.06e-37

chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 homolog beta (also known as HP1beta, Cbx1, chromobox 1) is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1beta has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1beta may play an important role in the epigenetic control of chromatin structure and gene expression. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3


:

Pssm-ID: 349301  Cd Length: 58  Bit Score: 119.43  E-value: 1.06e-37
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*...
1DZ1_B      11 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 68
Cdd:cd18654  1 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 58
 
Name Accession Description Interval E-value
CSD_HP1beta_Cbx1 cd18654
chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 ...
11-68 1.06e-37

chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 homolog beta (also known as HP1beta, Cbx1, chromobox 1) is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1beta has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1beta may play an important role in the epigenetic control of chromatin structure and gene expression. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3


Pssm-ID: 349301  Cd Length: 58  Bit Score: 119.43  E-value: 1.06e-37
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*...
1DZ1_B      11 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 68
Cdd:cd18654  1 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 58
Chromo_shadow pfam01393
Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always ...
17-69 5.49e-34

Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always found in association with a chromo domain.


Pssm-ID: 334521  Cd Length: 53  Bit Score: 109.53  E-value: 5.49e-34
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
1DZ1_B        17 EPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTW 69
Cdd:pfam01393  1 EPEKIVGATDTNGELMFLIKWKNGEEADLVPAKEANQKCPQKVIKFYEERLVW 53
ChSh smart00300
Chromo Shadow Domain;
10-70 1.97e-32

Chromo Shadow Domain;


Pssm-ID: 197638  Cd Length: 61  Bit Score: 105.92  E-value: 1.97e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
1DZ1_B         10 RGFARGLEPERIIGATDSSGELMFLMKWKNsDEADLVPAKEANVKCPQVVISFYEERLTWH 70
Cdd:smart00300  1 KGFERGKSWEDIVGATKDDGELTFLIKWKD-DAASLVPSKEANVKCPQMVIRFYEEHLTFQ 60
 
Name Accession Description Interval E-value
CSD_HP1beta_Cbx1 cd18654
chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 ...
11-68 1.06e-37

chromo shadow domain of heterochromatin protein 1 homolog beta; heterochromatin protein 1 homolog beta (also known as HP1beta, Cbx1, chromobox 1) is a highly conserved non-histone protein, which is a member of the heterochromatin protein family, and is enriched in the heterochromatin and associated with centromeres. HP1beta has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1beta may play an important role in the epigenetic control of chromatin structure and gene expression. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta, and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3


Pssm-ID: 349301  Cd Length: 58  Bit Score: 119.43  E-value: 1.06e-37
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*...
1DZ1_B      11 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 68
Cdd:cd18654  1 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 58
Chromo_shadow pfam01393
Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always ...
17-69 5.49e-34

Chromo shadow domain; This domain is distantly related to pfam00385. This domain is always found in association with a chromo domain.


Pssm-ID: 334521  Cd Length: 53  Bit Score: 109.53  E-value: 5.49e-34
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
1DZ1_B        17 EPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLTW 69
Cdd:pfam01393  1 EPEKIVGATDTNGELMFLIKWKNGEEADLVPAKEANQKCPQKVIKFYEERLVW 53
CSD_HP1gamma_Cbx3 cd18656
chromo shadow domain of heterochromatin protein 1 gamma homolog gamma; Chromo shadow domain ...
11-68 5.69e-34

chromo shadow domain of heterochromatin protein 1 gamma homolog gamma; Chromo shadow domain (CSD) of heterochromatin protein 1 gamma homolog gamma (also known as HP1gamma, Cbx3, Chromobox 3), and related proteins. HP1gamma appears to be involved in transcriptional silencing in heterochromatin-like complexes. It binds histone H3 tails methylated at Lys-9, leading to epigenetic repression, and also binds lamin B receptor, an integral membrane protein found in the inner nuclear membrane. The dual binding functions of the protein may explain the association of heterochromatin with the inner nuclear membrane. HP1gamma is also recruited to sites of ultraviolet-induced DNA damage and double-strand breaks. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal CSD which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma. The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


Pssm-ID: 349303  Cd Length: 58  Bit Score: 109.78  E-value: 5.69e-34
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*...
1DZ1_B      11 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 68
Cdd:cd18656  1 GFARGLDPERIIGATDSSGELMFLMKWKDSDEADLVLAKEANMKCPQIVIAFYEERLT 58
ChSh smart00300
Chromo Shadow Domain;
10-70 1.97e-32

Chromo Shadow Domain;


Pssm-ID: 197638  Cd Length: 61  Bit Score: 105.92  E-value: 1.97e-32
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
1DZ1_B         10 RGFARGLEPERIIGATDSSGELMFLMKWKNsDEADLVPAKEANVKCPQVVISFYEERLTWH 70
Cdd:smart00300  1 KGFERGKSWEDIVGATKDDGELTFLIKWKD-DAASLVPSKEANVKCPQMVIRFYEEHLTFQ 60
CSD cd00034
chromo shadow domain; The chromo shadow domain (CSD) is always found in association with a ...
16-67 2.50e-32

chromo shadow domain; The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. CSDs are found for example in Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


Pssm-ID: 349275  Cd Length: 52  Bit Score: 105.37  E-value: 2.50e-32
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|..
1DZ1_B      16 LEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERL 67
Cdd:cd00034  1 LEVEKILGATDSDGELMFLIKWKGSDEADLVPAKEANEKCPQIVIQFYESRL 52
CSD_HP1alpha_Cbx5 cd18655
chromo shadow domain of heterochromatin protein 1 homolog alpha; Chromo shadow domain (CSD) of ...
11-68 9.69e-32

chromo shadow domain of heterochromatin protein 1 homolog alpha; Chromo shadow domain (CSD) of heterochromatin protein 1 homolog alpha (also known as HP1alpha, Cbx5, and Chromobox 5), and related proteins. HP1alpha has diverse functions in heterochromatin formation, gene regulation, and mitotic progression, and forms complex networks of gene, RNA, and protein interactions. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. CSD domains have only been found in proteins that also possess a related chromodomain, while chromodomains can exist in isolation. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha, HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


Pssm-ID: 349302  Cd Length: 58  Bit Score: 104.32  E-value: 9.69e-32
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*...
1DZ1_B      11 GFARGLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERLT 68
Cdd:cd18655  1 GFERGLEPEKIIGATDSCGDLMFLMKWKDSDEADLVLAKEANVKCPQIVIAFYEERLT 58
CSD_HP1a_insect cd18658
chromo shadow domain of insect heterochromatin protein 1a; The chromo shadow domain (CSD) is ...
15-67 2.26e-21

chromo shadow domain of insect heterochromatin protein 1a; The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal CSD which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3. In Drosophila, there are at least five HP1 family proteins, this subgroup includes the CSD of Drosophila melanogaster HP1a.


Pssm-ID: 349305  Cd Length: 53  Bit Score: 78.12  E-value: 2.26e-21
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|...
1DZ1_B      15 GLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERL 67
Cdd:cd18658  1 GLEAEKILGASDSNGGLTFLIQFKGVDQAEMVPASVANVKIPQMVIKFYEERL 53
CSD_Swi6 cd18657
chromo shadow domain of chromatin-associated protein Swi6; Chromo shadow domain (CSD) of ...
25-67 6.89e-11

chromo shadow domain of chromatin-associated protein Swi6; Chromo shadow domain (CSD) of fission yeast Swi6 protein. Swi6 is a structural and functional homolog of mammalian HP1 (heterochromatin protein 1) and is involved in the chromatin structure by binding to centromere, telomere and silent mating-type locus. Swi6 contains a N-terminal chromo (CHRromatin Organization MOdifier) domain and a C-terminal chromo shadow domain (CSD). Swi6 binds histone H3 tails methylated at Lys- and the cohesion subunit Psc3, leading to silencing the genes and sister chromatid cohesion. It is also involved in the repression of the silent mating-type loci MAT2 and MAT3. Swi6 may compact MAT2/3 into a heterochromatin-like conformation which represses the transcription of these silent cassettes. The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation.


Pssm-ID: 349304  Cd Length: 55  Bit Score: 51.52  E-value: 6.89e-11
                       10        20        30        40
               ....*....|....*....|....*....|....*....|...
1DZ1_B      25 TDSSGELMFLMKWKNSDEAdLVPAKEANVKCPQVVISFYEERL 67
Cdd:cd18657 14 RDKDGKLLVYLTWKNGKKS-QHPSSVVYKKCPQKMLQFYESHL 55
CSD_HP1e_insect cd18981
chromo shadow domain of insect heterochromatin protein 1E; The chromo shadow domain (CSD) is ...
15-67 1.58e-08

chromo shadow domain of insect heterochromatin protein 1E; The chromo shadow domain (CSD) is always found in association with a related N-terminal chromo (CHRromatin Organization MOdifier) domain. CSD domains have only been found in proteins that also possess a chromodomain, while chromodomains can exist in isolation. CSDs are found for example in Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2. HP1 is a highly conserved non-histone chromosomal protein that is evolutionarily conserved from fission yeast to plants and animals. HP1 has two conserved protein-protein interaction domains, a single N-terminal chromodomain (CD) which can bind to histone proteins via methylated lysine residues, and a related C-terminal chromo shadow domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated non-histone proteins; a flexible hinge region separates the CD and CSD and may bind nucleic acid. The HP1 CSD, in addition to interacting with various proteins bearing the PXVXL motif, also interacts with a region of histone H3 that bears the similar PXXVXL motif. There are three human homologs of HP1 proteins: HP1alpha (also known as Cbx5), HP1beta (also known as Cbx1), and HP1gamma (also known as Cbx3). The CSD domains of all three human HP1 homologs have similar affinities to the PXXVXL motif of histone H3.


Pssm-ID: 349337  Cd Length: 53  Bit Score: 45.23  E-value: 1.58e-08
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|...
1DZ1_B      15 GLEPERIIGATDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEERL 67
Cdd:cd18981  1 GFTAQEILKGINNNGEISFLIRFKHLDQPQVVPSDMAYVEIPQMVLKFYENHC 53
CHROMO smart00298
Chromatin organization modifier domain;
17-66 4.24e-04

Chromatin organization modifier domain;


Pssm-ID: 214605 [Multi-domain]  Cd Length: 55  Bit Score: 34.11  E-value: 4.24e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
1DZ1_B         17 EPERIIGA-TDSSGELMFLMKWKNSDEADLVPAKEANVKCPQVVISFYEER 66
Cdd:smart00298  3 EVEKILDHrWKKKGELEYLVKWKGYSYSEDTWEPEENLLNCSKKLDNYKKK 53
CD_CSD cd00024
CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this ...
17-65 1.79e-03

CHROMO (CHRromatin Organization Modifier) domains and chromo shadow domains; Members of this group are chromodomains or chromo shadow domains; these are SH3-fold-beta-barrel domains of the chromo-like superfamily. Chromodomains lack the first strand of the SH3-fold-beta-barrel, this first strand is altered by insertion in the chromo shadow domains. The chromodomain is a conserved region of about 50 amino acids, found in a variety of chromosomal proteins, and which appears to play a role in the functional organization of the eukaryotic nucleus. The chromodomain is implicated in the binding, of the proteins in which it is found, to methylated histone tails and maybe RNA. Chromodomain-containing proteins include: i) those having an N-terminal chromodomain followed by a related chromo shadow domain, such as Drosophila and human heterochromatin protein Su(var)205 (HP1), and mammalian modifier 1 and 2; ii) those having a single chromodomain, such as Drosophila protein Polycomb (Pc), mammalian modifier 3, human Mi-2 autoantigen, and several yeast and Caenorhabditis elegans proteins of unknown function; iii) those having paired tandem chromodomains, such as mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1; (iv) and elongation factor eEF3, a member of the ATP-binding cassette (ABC) family of proteins, that serves an essential function in the translation cycle of fungi. eEF3 is a soluble factor lacking a transmembrane domain and having two ABC domains arranged in tandem, with a unique chromodomain inserted within the ABC2 domain.


Pssm-ID: 349274  Cd Length: 50  Bit Score: 32.45  E-value: 1.79e-03
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|.
1DZ1_B      17 EPERIIGATDSSGELMFLMKWKNSDEAD--LVPakEANVKCPQVVISFYEE 65
Cdd:cd00024  2 EVEKILDHRVRKGKLEYLVKWKGYPPEEntWEP--EENLTNAPELIKEYEK 50
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.17
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
  • Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.
  • Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.
  • Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.
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