Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8WHA

Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0005576	cellular_component	extracellular region
A	0005634	cellular_component	nucleus
A	0005694	cellular_component	chromosome
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0009536	cellular_component	plastid
A	0010369	cellular_component	chromocenter
B	0000325	cellular_component	plant-type vacuole
B	0000786	cellular_component	nucleosome
B	0003677	molecular_function	DNA binding
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005634	cellular_component	nucleus
B	0005694	cellular_component	chromosome
B	0005730	cellular_component	nucleolus
B	0005777	cellular_component	peroxisome
B	0005794	cellular_component	Golgi apparatus
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0009414	biological_process	response to water deprivation
B	0009506	cellular_component	plasmodesma
B	0009507	cellular_component	chloroplast
B	0009536	cellular_component	plastid
B	0009579	cellular_component	thylakoid
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
C	0005730	cellular_component	nucleolus
C	0009294	biological_process	DNA-mediated transformation
C	0009536	cellular_component	plastid
C	0009611	biological_process	response to wounding
C	0009617	biological_process	response to bacterium
D	0000786	cellular_component	nucleosome
D	0003677	molecular_function	DNA binding
D	0005634	cellular_component	nucleus
D	0005694	cellular_component	chromosome
D	0005730	cellular_component	nucleolus
D	0005829	cellular_component	cytosol
D	0009534	cellular_component	chloroplast thylakoid
D	0009570	cellular_component	chloroplast stroma
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0005515	molecular_function	protein binding
E	0005576	cellular_component	extracellular region
E	0005634	cellular_component	nucleus
E	0005694	cellular_component	chromosome
E	0005829	cellular_component	cytosol
E	0005886	cellular_component	plasma membrane
E	0009536	cellular_component	plastid
E	0010369	cellular_component	chromocenter
F	0000325	cellular_component	plant-type vacuole
F	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0005515	molecular_function	protein binding
F	0005576	cellular_component	extracellular region
F	0005634	cellular_component	nucleus
F	0005694	cellular_component	chromosome
F	0005730	cellular_component	nucleolus
F	0005777	cellular_component	peroxisome
F	0005794	cellular_component	Golgi apparatus
F	0005829	cellular_component	cytosol
F	0005886	cellular_component	plasma membrane
F	0009414	biological_process	response to water deprivation
F	0009506	cellular_component	plasmodesma
F	0009507	cellular_component	chloroplast
F	0009536	cellular_component	plastid
F	0009579	cellular_component	thylakoid
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005694	cellular_component	chromosome
G	0005730	cellular_component	nucleolus
G	0009294	biological_process	DNA-mediated transformation
G	0009536	cellular_component	plastid
G	0009611	biological_process	response to wounding
G	0009617	biological_process	response to bacterium
H	0000786	cellular_component	nucleosome
H	0003677	molecular_function	DNA binding
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0005730	cellular_component	nucleolus
H	0005829	cellular_component	cytosol
H	0009534	cellular_component	chloroplast thylakoid
H	0009570	cellular_component	chloroplast stroma
K	0000786	cellular_component	nucleosome
K	0003677	molecular_function	DNA binding
K	0003678	molecular_function	DNA helicase activity
K	0004386	molecular_function	helicase activity
K	0005515	molecular_function	protein binding
K	0005524	molecular_function	ATP binding
K	0005634	cellular_component	nucleus
K	0006338	biological_process	chromatin remodeling
K	0006346	biological_process	DNA methylation-dependent heterochromatin formation
K	0009294	biological_process	DNA-mediated transformation
K	0016787	molecular_function	hydrolase activity
K	0016887	molecular_function	ATP hydrolysis activity
K	0031507	biological_process	heterochromatin formation
K	0032197	biological_process	retrotransposition
K	0032508	biological_process	DNA duplex unwinding
K	0040029	biological_process	epigenetic regulation of gene expression
L	0000786	cellular_component	nucleosome
L	0003677	molecular_function	DNA binding
L	0003678	molecular_function	DNA helicase activity
L	0004386	molecular_function	helicase activity
L	0005515	molecular_function	protein binding
L	0005524	molecular_function	ATP binding
L	0005634	cellular_component	nucleus
L	0006338	biological_process	chromatin remodeling
L	0006346	biological_process	DNA methylation-dependent heterochromatin formation
L	0009294	biological_process	DNA-mediated transformation
L	0016787	molecular_function	hydrolase activity
L	0016887	molecular_function	ATP hydrolysis activity
L	0031507	biological_process	heterochromatin formation
L	0032197	biological_process	retrotransposition
L	0032508	biological_process	DNA duplex unwinding
L	0040029	biological_process	epigenetic regulation of gene expression

Functional Information from PROSITE/UniProt

site_id	PS00046
Number of Residues	7
Details	HISTONE_H2A Histone H2A signature. AGLqFPV

Chain	Residue	Details
C	ALA22-VAL28

site_id	PS00047
Number of Residues	5
Details	HISTONE_H4 Histone H4 signature. GAKRH

Chain	Residue	Details
B	GLY14-HIS18

site_id	PS00322
Number of Residues	7
Details	HISTONE_H3_1 Histone H3 signature 1. KAPRKQL

Chain	Residue	Details
A	LYS14-LEU20

site_id	PS00357
Number of Residues	23
Details	HISTONE_H2B Histone H2B signature. REIQTavRlVLpGELaKHAVSEG

Chain	Residue	Details
D	ARG117-GLY139

site_id	PS00959
Number of Residues	9
Details	HISTONE_H3_2 Histone H3 signature 2. PFqRLVREI

Chain	Residue	Details
A	PRO66-ILE74

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	BINDING: BINDING => ECO:0000255\|PROSITE-ProRule:PRU00541

Chain	Residue	Details
K	ASP227
L	ASP227

site_id	SWS_FT_FI2
Number of Residues	10
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:17691833

Chain	Residue	Details
D	LYS6
H	LYS38
D	LYS11
D	LYS27
D	LYS32
D	LYS38
H	LYS6
H	LYS11
H	LYS27
H	LYS32

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000250\|UniProtKB:Q9FFC0

Chain	Residue	Details
D	LYS12
H	LYS12

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: N6-acetyllysine; partial => ECO:0000269\|PubMed:17691833

Chain	Residue	Details
D	LYS39
H	LYS39

site_id	SWS_FT_FI5
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000250\|UniProtKB:Q9LQQ4

Chain	Residue	Details
D	LYS145
E	LYS9
H	LYS145

site_id	SWS_FT_FI6
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000269\|PubMed:14610360, ECO:0000269\|PubMed:15753571

Chain	Residue	Details
A	SER10
A	SER28
E	SER10
E	SER28

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0000269\|PubMed:15753571

Chain	Residue	Details
A	THR11
E	THR11

site_id	SWS_FT_FI8
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:15598823, ECO:0000269\|PubMed:16648464, ECO:0000269\|PubMed:17174094, ECO:0000269\|PubMed:17363895

Chain	Residue	Details
A	LYS14
E	LYS14

site_id	SWS_FT_FI9
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:15598823

Chain	Residue	Details
A	LYS18
A	LYS23
E	LYS18
E	LYS23

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:14712277, ECO:0000269\|PubMed:15598823, ECO:0000269\|PubMed:17174094, ECO:0000269\|PubMed:17439305, ECO:0000269\|PubMed:19503079, ECO:0000269\|PubMed:24626927, ECO:0000269\|PubMed:35298257

Chain	Residue	Details
A	LYS27
E	LYS27

site_id	SWS_FT_FI11
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:15598823, ECO:0000269\|PubMed:16299497

Chain	Residue	Details
A	LYS36
E	LYS36

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)