9E3U | pdb_00009e3u

Cryo-EM structure of DNMT 3A2/3B3 tetramer bound to a di-nucleosome with a 25 base-pair linker


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCore histone-like 8070545 3001387 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyCore histone-like 8070531 3001387 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B, F
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-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 asso ...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 [2-3].
Domain
N [auth U],
O [auth Y]
PF21255DNMT3, ADD PHD zinc finger (DNMT3_ADD_GATA1-like)DNMT3, ADD PHD zinc fingerDNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc fin ...DNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc finger, represented in this entry. In this domain, the conserved His residue observed in classical PHD zinc fingers is replaced by a cysteine.
Domain
N [auth U],
O [auth Y]
PF00145C-5 cytosine-specific DNA methylase (DNA_methylase)C-5 cytosine-specific DNA methylaseDomain
I [auth L],
L [auth V],
M [auth Z]
PF21255DNMT3, ADD PHD zinc finger (DNMT3_ADD_GATA1-like)DNMT3, ADD PHD zinc fingerDNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc fin ...DNMT3s are de novo DNA methyltransferases responsible for the establishment of DNA methylation patterns in mammalian genomes [1-4]. The ATRX-DNMT3-DNMT3L (ADD) domain contains two parts, a C2-C2-like zinc finger (Pfam:PF17980) and a PHD-like zinc finger, represented in this entry. In this domain, the conserved His residue observed in classical PHD zinc fingers is replaced by a cysteine.
Domain
I [auth L],
L [auth V],
M [auth Z]
PF17980DNMT3, cysteine rich ADD domain, GATA1-like zinc finger (ADD_DNMT3)DNMT3, cysteine rich ADD domain, GATA1-like zinc fingerThis is a C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome ...This is a C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome with chromatin containing methylated H3K4. This domain contains two parts, a GATA1-like and a PHD-like (Pfam:PF21255) zinc fingers. The DNA methyltransferase (DNMT) 3 family members DNMT3A and the DNMT3-like non-enzymatic regulatory factor DNMT3L, are involved in de-novo establishment of DNA methylation patterns in early mammalian development [1,2].
Domain
I [auth L],
L [auth V],
M [auth Z]
PF00145C-5 cytosine-specific DNA methylase (DNA_methylase)C-5 cytosine-specific DNA methylaseDomain
A, E
PF00125Core histone H2A/H2B/H3/H4 domain (Histone)Core histone H2A/H2B/H3/H4 domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B, F
Histone H4
C, G
Histone H2A---
J [auth I]DNA (165-MER)---
K [auth J]DNA (165-MER)---
N [auth U],
O [auth Y]
DNA (cytosine-5)-methyltransferase 3A
I [auth L],
L [auth V],
M [auth Z]
Isoform 3 of DNA (cytosine-5)-methyltransferase 3B
D, H
Histone H2B
A, E
Histone H3.2

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B, F
IPR009072Histone-foldHomologous Superfamily
B, F
IPR035425CENP-T/Histone H4, histone foldDomain
B, F
IPR001951Histone H4Family
B, F
IPR019809Histone H4, conserved siteConserved Site
B, F
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
N [auth U],
O [auth Y]
IPR040552DNMT3, cysteine rich ADD domain, GATA1-like zinc fingerDomain
N [auth U],
O [auth Y]
IPR044108DNA (cytosine-5)-methyltransferase 3A, ADD domainDomain
N [auth U],
O [auth Y]
IPR000313PWWP domainDomain
N [auth U],
O [auth Y]
IPR018117DNA methylase, C-5 cytosine-specific, active siteActive Site
N [auth U],
O [auth Y]
IPR049554DNMT3, ADD domain, PHD zinc fingerDomain
N [auth U],
O [auth Y]
IPR001525C-5 cytosine methyltransferaseFamily
N [auth U],
O [auth Y]
IPR054724DNA (cytosine-5)-methyltransferase, N-terminalDomain
N [auth U],
O [auth Y]
IPR025766ADD domainDomain
N [auth U],
O [auth Y]
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
N [auth U],
O [auth Y]
IPR050390DNA Cytosine-5 MethyltransferaseFamily
I [auth L],
L [auth V],
M [auth Z]
IPR040552DNMT3, cysteine rich ADD domain, GATA1-like zinc fingerDomain
I [auth L],
L [auth V],
M [auth Z]
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
I [auth L],
L [auth V],
M [auth Z]
IPR049554DNMT3, ADD domain, PHD zinc fingerDomain
I [auth L],
L [auth V],
M [auth Z]
IPR050390DNA Cytosine-5 MethyltransferaseFamily
I [auth L],
L [auth V],
M [auth Z]
IPR000313PWWP domainDomain
I [auth L],
L [auth V],
M [auth Z]
IPR030488DNA (cytosine-5)-methyltransferase 3B, ADD domainDomain
I [auth L],
L [auth V],
M [auth Z]
IPR018117DNA methylase, C-5 cytosine-specific, active siteActive Site
I [auth L],
L [auth V],
M [auth Z]
IPR001525C-5 cytosine methyltransferaseFamily
I [auth L],
L [auth V],
M [auth Z]
IPR011011Zinc finger, FYVE/PHD-typeHomologous Superfamily
I [auth L],
L [auth V],
M [auth Z]
IPR025766ADD domainDomain
D, H
IPR009072Histone-foldHomologous Superfamily
D, H
IPR000558Histone H2BFamily
D, H
IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
D, H
IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
D, H
IPR007125Core Histone H2A/H2B/H3 domainDomain
D, H
IPR055333Histone H2B, conserved siteConserved Site
D, H
IPR005818Linker histone H1/H5, domain H15Domain
A, E
IPR009072Histone-foldHomologous Superfamily
A, E
IPR007125Core Histone H2A/H2B/H3 domainDomain
A, E
IPR000164Histone H3/CENP-AFamily

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
B, F
PharosP62805
N [auth U],
O [auth Y]
PharosQ9Y6K1
I [auth L],
L [auth V],
M [auth Z]
PharosQ9UBC3
A, E
PharosQ71DI3