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8QZM

Structure of DNMT3A1 UDR region bound to H2AK119ub nucleosome

Functional Information from GO Data
ChainGOidnamespacecontents
A0000786cellular_componentnucleosome
A0003677molecular_functionDNA binding
A0005634cellular_componentnucleus
A0005694cellular_componentchromosome
A0030527molecular_functionstructural constituent of chromatin
A0046982molecular_functionprotein heterodimerization activity
B0000781cellular_componentchromosome, telomeric region
B0000786cellular_componentnucleosome
B0003677molecular_functionDNA binding
B0003723molecular_functionRNA binding
B0005515molecular_functionprotein binding
B0005576cellular_componentextracellular region
B0005634cellular_componentnucleus
B0005654cellular_componentnucleoplasm
B0005694cellular_componentchromosome
B0006325biological_processchromatin organization
B0006334biological_processnucleosome assembly
B0016020cellular_componentmembrane
B0030527molecular_functionstructural constituent of chromatin
B0032200biological_processtelomere organization
B0032991cellular_componentprotein-containing complex
B0043505cellular_componentCENP-A containing nucleosome
B0045653biological_processnegative regulation of megakaryocyte differentiation
B0046982molecular_functionprotein heterodimerization activity
B0061644biological_processprotein localization to CENP-A containing chromatin
B0070062cellular_componentextracellular exosome
C0000786cellular_componentnucleosome
C0003677molecular_functionDNA binding
C0005515molecular_functionprotein binding
C0005634cellular_componentnucleus
C0005694cellular_componentchromosome
C0019899molecular_functionenzyme binding
C0030527molecular_functionstructural constituent of chromatin
C0031507biological_processheterochromatin formation
C0046982molecular_functionprotein heterodimerization activity
C0070062cellular_componentextracellular exosome
D0000786cellular_componentnucleosome
D0002227biological_processinnate immune response in mucosa
D0003677molecular_functionDNA binding
D0005515molecular_functionprotein binding
D0005615cellular_componentextracellular space
D0005634cellular_componentnucleus
D0005654cellular_componentnucleoplasm
D0005694cellular_componentchromosome
D0005829cellular_componentcytosol
D0006334biological_processnucleosome assembly
D0019731biological_processantibacterial humoral response
D0030527molecular_functionstructural constituent of chromatin
D0042742biological_processdefense response to bacterium
D0042802molecular_functionidentical protein binding
D0046982molecular_functionprotein heterodimerization activity
D0050830biological_processdefense response to Gram-positive bacterium
D0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
D0070062cellular_componentextracellular exosome
E0000786cellular_componentnucleosome
E0003677molecular_functionDNA binding
E0005634cellular_componentnucleus
E0005694cellular_componentchromosome
E0030527molecular_functionstructural constituent of chromatin
E0046982molecular_functionprotein heterodimerization activity
F0000781cellular_componentchromosome, telomeric region
F0000786cellular_componentnucleosome
F0003677molecular_functionDNA binding
F0003723molecular_functionRNA binding
F0005515molecular_functionprotein binding
F0005576cellular_componentextracellular region
F0005634cellular_componentnucleus
F0005654cellular_componentnucleoplasm
F0005694cellular_componentchromosome
F0006325biological_processchromatin organization
F0006334biological_processnucleosome assembly
F0016020cellular_componentmembrane
F0030527molecular_functionstructural constituent of chromatin
F0032200biological_processtelomere organization
F0032991cellular_componentprotein-containing complex
F0043505cellular_componentCENP-A containing nucleosome
F0045653biological_processnegative regulation of megakaryocyte differentiation
F0046982molecular_functionprotein heterodimerization activity
F0061644biological_processprotein localization to CENP-A containing chromatin
F0070062cellular_componentextracellular exosome
G0000786cellular_componentnucleosome
G0003677molecular_functionDNA binding
G0005515molecular_functionprotein binding
G0005634cellular_componentnucleus
G0005694cellular_componentchromosome
G0019899molecular_functionenzyme binding
G0030527molecular_functionstructural constituent of chromatin
G0031507biological_processheterochromatin formation
G0046982molecular_functionprotein heterodimerization activity
G0070062cellular_componentextracellular exosome
H0000786cellular_componentnucleosome
H0002227biological_processinnate immune response in mucosa
H0003677molecular_functionDNA binding
H0005515molecular_functionprotein binding
H0005615cellular_componentextracellular space
H0005634cellular_componentnucleus
H0005654cellular_componentnucleoplasm
H0005694cellular_componentchromosome
H0005829cellular_componentcytosol
H0006334biological_processnucleosome assembly
H0019731biological_processantibacterial humoral response
H0030527molecular_functionstructural constituent of chromatin
H0042742biological_processdefense response to bacterium
H0042802molecular_functionidentical protein binding
H0046982molecular_functionprotein heterodimerization activity
H0050830biological_processdefense response to Gram-positive bacterium
H0061844biological_processantimicrobial humoral immune response mediated by antimicrobial peptide
H0070062cellular_componentextracellular exosome
K0000122biological_processnegative regulation of transcription by RNA polymerase II
K0000775cellular_componentchromosome, centromeric region
K0000791cellular_componenteuchromatin
K0000792cellular_componentheterochromatin
K0000978molecular_functionRNA polymerase II cis-regulatory region sequence-specific DNA binding
K0001741cellular_componentXY body
K0003677molecular_functionDNA binding
K0003682molecular_functionchromatin binding
K0003714molecular_functiontranscription corepressor activity
K0003886molecular_functionDNA (cytosine-5-)-methyltransferase activity
K0005515molecular_functionprotein binding
K0005634cellular_componentnucleus
K0005654cellular_componentnucleoplasm
K0005694cellular_componentchromosome
K0005737cellular_componentcytoplasm
K0006325biological_processchromatin organization
K0006346biological_processDNA methylation-dependent constitutive heterochromatin formation
K0007283biological_processspermatogenesis
K0008168molecular_functionmethyltransferase activity
K0008270molecular_functionzinc ion binding
K0009410biological_processresponse to xenobiotic stimulus
K0009636biological_processresponse to toxic substance
K0009791biological_processpost-embryonic development
K0010212biological_processresponse to ionizing radiation
K0010288biological_processresponse to lead ion
K0010468biological_processregulation of gene expression
K0016363cellular_componentnuclear matrix
K0016740molecular_functiontransferase activity
K0030182biological_processneuron differentiation
K0031048biological_processregulatory ncRNA-mediated heterochromatin formation
K0031507biological_processheterochromatin formation
K0031667biological_processresponse to nutrient levels
K0032259biological_processmethylation
K0032355biological_processresponse to estradiol
K0033189biological_processresponse to vitamin A
K0042220biological_processresponse to cocaine
K0042802molecular_functionidentical protein binding
K0043045biological_processepigenetic programming of gene expression
K0044027biological_processnegative regulation of gene expression via chromosomal CpG island methylation
K0045322molecular_functionunmethylated CpG binding
K0045471biological_processresponse to ethanol
K0045892biological_processnegative regulation of DNA-templated transcription
K0046872molecular_functionmetal ion binding
K0061629molecular_functionRNA polymerase II-specific DNA-binding transcription factor binding
K0071230biological_processcellular response to amino acid stimulus
K0071361biological_processcellular response to ethanol
K0071456biological_processcellular response to hypoxia
K0071514biological_processgenomic imprinting
K0097284biological_processhepatocyte apoptotic process
K0106222molecular_functionlncRNA binding
K0106363molecular_functionprotein-cysteine methyltransferase activity
K0141068biological_processautosome genomic imprinting
K0141196biological_processtransposable element silencing by piRNA-mediated DNA methylation
K1900039biological_processpositive regulation of cellular response to hypoxia
K1902494cellular_componentcatalytic complex
K1903926biological_processcellular response to bisphenol A
Functional Information from PROSITE/UniProt
site_idPS00046
Number of Residues7
DetailsHISTONE_H2A Histone H2A signature. AGLqFPV
ChainResidueDetails
CALA21-VAL27

site_idPS00047
Number of Residues5
DetailsHISTONE_H4 Histone H4 signature. GAKRH
ChainResidueDetails
BGLY14-HIS18

site_idPS00094
Number of Residues13
DetailsC5_MTASE_1 C-5 cytosine-specific DNA methylases active site. DlVigGsPCnDLS
ChainResidueDetails
KASP702-SER714

site_idPS00322
Number of Residues7
DetailsHISTONE_H3_1 Histone H3 signature 1. KAPRKQL
ChainResidueDetails
ALYS14-LEU20

site_idPS00357
Number of Residues23
DetailsHISTONE_H2B Histone H2B signature. REIQTavRlLLpGELaKHAVSEG
ChainResidueDetails
DARG92-GLY114

site_idPS00959
Number of Residues9
DetailsHISTONE_H3_2 Histone H3 signature 2. PFqRLVREI
ChainResidueDetails
APRO66-ILE74

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues30
DetailsZN_FING: GATA-type; atypical => ECO:0000255|PROSITE-ProRule:PRU00865
ChainResidueDetails
KILE493-GLU523
HPRO1

site_idSWS_FT_FI2
Number of Residues56
DetailsZN_FING: PHD-type; atypical => ECO:0000255|PROSITE-ProRule:PRU00865
ChainResidueDetails
KGLN534-GLY590
HGLU2

site_idSWS_FT_FI3
Number of Residues1
DetailsACT_SITE: ACT_SITE => ECO:0000255|PROSITE-ProRule:PRU01016, ECO:0000255|PROSITE-ProRule:PRU10018
ChainResidueDetails
KCYS710
HLYS11
HLYS15
HLYS16
HLYS20
HLYS23
HLYS43
HLYS85
DLYS11
DLYS15
DLYS16
DLYS20
DLYS23
DLYS43
DLYS85
HLYS5

site_idSWS_FT_FI4
Number of Residues4
DetailsBINDING: BINDING => ECO:0000269|PubMed:17713477, ECO:0007744|PDB:2QRV
ChainResidueDetails
KASP641
KGLU664
KASP686
KARG891

site_idSWS_FT_FI5
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163
ChainResidueDetails
KSER105
HLYS12
BLYS44
FLYS8
FLYS16
FLYS44

site_idSWS_FT_FI6
Number of Residues1
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q1LZ53
ChainResidueDetails
KTHR124
HSER14
BLYS77
BLYS91
FLYS12
FLYS31
FLYS77
FLYS91

site_idSWS_FT_FI7
Number of Residues1
DetailsMOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:O88508
ChainResidueDetails
KARG171
HLYS24

site_idSWS_FT_FI8
Number of Residues1
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692
ChainResidueDetails
KSER243
DLYS116
DLYS120
HLYS34
HLYS116
HLYS120

site_idSWS_FT_FI9
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0007744|PubMed:21406692
ChainResidueDetails
KSER255
KSER267
CLYS125
GLYS118
GCYS119
GLYS125

site_idSWS_FT_FI10
Number of Residues1
DetailsMOD_RES: Phosphothreonine => ECO:0007744|PubMed:21406692
ChainResidueDetails
KTHR261
HSER36

site_idSWS_FT_FI11
Number of Residues2
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:O88508
ChainResidueDetails
KSER390
KSER393
HLYS46
HLYS108

site_idSWS_FT_FI12
Number of Residues1
DetailsMOD_RES: S-methylcysteine; by autocatalysis => ECO:0000250|UniProtKB:O88508
ChainResidueDetails
KCYS710
HLYS57
GCYS119

site_idSWS_FT_FI13
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733
ChainResidueDetails
KLYS162
HARG79

site_idSWS_FT_FI14
Number of Residues4
DetailsMOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08
ChainResidueDetails
DARG86
DARG92
HARG86
HARG92

site_idSWS_FT_FI15
Number of Residues2
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729
ChainResidueDetails
DTHR115
HTHR115
FLYS91

site_idSWS_FT_FI16
Number of Residues2
DetailsCARBOHYD: O-linked (GlcNAc) serine => ECO:0000269|PubMed:22121020
ChainResidueDetails
DSER112
HSER112
BLYS79
FLYS20
FLYS59
FLYS79

site_idSWS_FT_FI17
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:P58876
ChainResidueDetails
DLYS5
HLYS5

site_idSWS_FT_FI18
Number of Residues4
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:16307923, ECO:0000269|PubMed:16627869, ECO:0000269|PubMed:16713563, ECO:0000269|PubMed:22121020
ChainResidueDetails
DLYS120
HLYS120

site_idSWS_FT_FI19
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:Q5QNW6
ChainResidueDetails
DLYS20
HLYS20

site_idSWS_FT_FI20
Number of Residues2
DetailsCROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816
ChainResidueDetails
DLYS34
HLYS34

237423

PDB entries from 2025-06-11

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