9MPP | pdb_00009mpp

The cryo-EM structure of nucleosome-bound DNA methyltransferases DNMT3A2 and DNMT3L


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyCore histone-like 8041272 3001387 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyCore histone-like 8041278 3001387 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyCore histone-like 8041278 3001387 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyCore histone-like 8041279 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
C, G
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- Family
K [auth M],
M [auth K]
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
K [auth M],
M [auth K]
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
K [auth M],
M [auth K]
PF00145C-5 cytosine-specific DNA methylase (DNA_methylase)C-5 cytosine-specific DNA methylaseDomain
L [auth N],
N [auth L]
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
L [auth N],
N [auth L]
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, E
Histone H3.2 -
B, F
Histone H4
C, G
Histone H2A type 1
D, H
Histone H2B 1.1 -
DNA (167-MER)---
DNA (167-MER)---
K [auth M],
M [auth K]
DNA (cytosine-5)-methyltransferase 3A
L [auth N],
N [auth L]
DNA (cytosine-5)-methyltransferase 3-like

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, E
IPR009072Histone-foldHomologous Superfamily
A, E
IPR000164Histone H3/CENP-AFamily
A, E
IPR007125Core Histone H2A/H2B/H3 domainDomain
B, F
IPR009072Histone-foldHomologous Superfamily
B, F
IPR001951Histone H4Family
B, F
IPR035425CENP-T/Histone H4, histone foldDomain
B, F
IPR019809Histone H4, conserved siteConserved Site
B, F
IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
C, G
IPR009072Histone-foldHomologous Superfamily
C, G
IPR002119Histone H2AFamily
C, G
IPR032454Histone H2A, C-terminal domainDomain
C, G
IPR032458Histone H2A conserved siteConserved Site
C, G
IPR007125Core Histone H2A/H2B/H3 domainDomain
D, H
IPR009072Histone-foldHomologous Superfamily
D, H
IPR055333Histone H2B, conserved siteConserved Site
D, H
IPR000558Histone H2BFamily
D, H
IPR007125Core Histone H2A/H2B/H3 domainDomain
K [auth M],
M [auth K]
IPR040552DNMT3, cysteine rich ADD domain, GATA1-like zinc fingerDomain
K [auth M],
M [auth K]
IPR044108DNA (cytosine-5)-methyltransferase 3A, ADD domainDomain
K [auth M],
M [auth K]
IPR000313PWWP domainDomain
K [auth M],
M [auth K]
IPR018117DNA methylase, C-5 cytosine-specific, active siteActive Site
K [auth M],
M [auth K]
IPR049554DNMT3, ADD domain, PHD zinc fingerDomain
K [auth M],
M [auth K]
IPR001525C-5 cytosine methyltransferaseFamily
K [auth M],
M [auth K]
IPR054724DNA (cytosine-5)-methyltransferase, N-terminalDomain
K [auth M],
M [auth K]
IPR025766ADD domainDomain
K [auth M],
M [auth K]
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
L [auth N],
N [auth L]
IPR040552DNMT3, cysteine rich ADD domain, GATA1-like zinc fingerDomain
L [auth N],
N [auth L]
IPR011011Zinc finger, FYVE/PHD-typeHomologous Superfamily
L [auth N],
N [auth L]
IPR029063S-adenosyl-L-methionine-dependent methyltransferase superfamilyHomologous Superfamily
L [auth N],
N [auth L]
IPR049554DNMT3, ADD domain, PHD zinc fingerDomain
L [auth N],
N [auth L]
IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
L [auth N],
N [auth L]
IPR025766ADD domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
K [auth M],
M [auth K]
PharosQ9Y6K1
L [auth N],
N [auth L]
PharosQ9UJW3