6FML

CryoEM Structure INO80core Nucleosome complex

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000492	biological_process	box C/D snoRNP assembly
A	0000812	cellular_component	Swr1 complex
A	0003678	molecular_function	DNA helicase activity
A	0004386	molecular_function	helicase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005634	cellular_component	nucleus
A	0006281	biological_process	DNA repair
A	0006325	biological_process	chromatin organization
A	0006338	biological_process	chromatin remodeling
A	0006357	biological_process	regulation of transcription by RNA polymerase II
A	0008094	molecular_function	ATP-dependent activity, acting on DNA
A	0016787	molecular_function	hydrolase activity
A	0016887	molecular_function	ATP hydrolysis activity
A	0031011	cellular_component	Ino80 complex
A	0032508	biological_process	DNA duplex unwinding
A	0035267	cellular_component	NuA4 histone acetyltransferase complex
A	0097255	cellular_component	R2TP complex
B	0000492	biological_process	box C/D snoRNP assembly
B	0000812	cellular_component	Swr1 complex
B	0003678	molecular_function	DNA helicase activity
B	0004386	molecular_function	helicase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005634	cellular_component	nucleus
B	0006281	biological_process	DNA repair
B	0006325	biological_process	chromatin organization
B	0006338	biological_process	chromatin remodeling
B	0006357	biological_process	regulation of transcription by RNA polymerase II
B	0008094	molecular_function	ATP-dependent activity, acting on DNA
B	0016787	molecular_function	hydrolase activity
B	0016887	molecular_function	ATP hydrolysis activity
B	0031011	cellular_component	Ino80 complex
B	0032508	biological_process	DNA duplex unwinding
B	0035267	cellular_component	NuA4 histone acetyltransferase complex
B	0097255	cellular_component	R2TP complex
C	0000492	biological_process	box C/D snoRNP assembly
C	0000812	cellular_component	Swr1 complex
C	0003678	molecular_function	DNA helicase activity
C	0004386	molecular_function	helicase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0005634	cellular_component	nucleus
C	0006281	biological_process	DNA repair
C	0006325	biological_process	chromatin organization
C	0006338	biological_process	chromatin remodeling
C	0006357	biological_process	regulation of transcription by RNA polymerase II
C	0008094	molecular_function	ATP-dependent activity, acting on DNA
C	0016787	molecular_function	hydrolase activity
C	0016887	molecular_function	ATP hydrolysis activity
C	0031011	cellular_component	Ino80 complex
C	0032508	biological_process	DNA duplex unwinding
C	0035267	cellular_component	NuA4 histone acetyltransferase complex
C	0097255	cellular_component	R2TP complex
D	0000492	biological_process	box C/D snoRNP assembly
D	0000812	cellular_component	Swr1 complex
D	0003678	molecular_function	DNA helicase activity
D	0004386	molecular_function	helicase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0006281	biological_process	DNA repair
D	0006325	biological_process	chromatin organization
D	0006338	biological_process	chromatin remodeling
D	0006357	biological_process	regulation of transcription by RNA polymerase II
D	0008094	molecular_function	ATP-dependent activity, acting on DNA
D	0016787	molecular_function	hydrolase activity
D	0016887	molecular_function	ATP hydrolysis activity
D	0031011	cellular_component	Ino80 complex
D	0032508	biological_process	DNA duplex unwinding
D	0035267	cellular_component	NuA4 histone acetyltransferase complex
D	0097255	cellular_component	R2TP complex
E	0000492	biological_process	box C/D snoRNP assembly
E	0000812	cellular_component	Swr1 complex
E	0003678	molecular_function	DNA helicase activity
E	0004386	molecular_function	helicase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0005634	cellular_component	nucleus
E	0006281	biological_process	DNA repair
E	0006325	biological_process	chromatin organization
E	0006338	biological_process	chromatin remodeling
E	0006357	biological_process	regulation of transcription by RNA polymerase II
E	0008094	molecular_function	ATP-dependent activity, acting on DNA
E	0016787	molecular_function	hydrolase activity
E	0016887	molecular_function	ATP hydrolysis activity
E	0031011	cellular_component	Ino80 complex
E	0032508	biological_process	DNA duplex unwinding
E	0035267	cellular_component	NuA4 histone acetyltransferase complex
E	0097255	cellular_component	R2TP complex
F	0000492	biological_process	box C/D snoRNP assembly
F	0000812	cellular_component	Swr1 complex
F	0003678	molecular_function	DNA helicase activity
F	0004386	molecular_function	helicase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0005634	cellular_component	nucleus
F	0006281	biological_process	DNA repair
F	0006325	biological_process	chromatin organization
F	0006338	biological_process	chromatin remodeling
F	0006357	biological_process	regulation of transcription by RNA polymerase II
F	0008094	molecular_function	ATP-dependent activity, acting on DNA
F	0016787	molecular_function	hydrolase activity
F	0016887	molecular_function	ATP hydrolysis activity
F	0031011	cellular_component	Ino80 complex
F	0032508	biological_process	DNA duplex unwinding
F	0035267	cellular_component	NuA4 histone acetyltransferase complex
F	0097255	cellular_component	R2TP complex
G	0003677	molecular_function	DNA binding
G	0005524	molecular_function	ATP binding
G	0005634	cellular_component	nucleus
G	0006281	biological_process	DNA repair
G	0006338	biological_process	chromatin remodeling
G	0006351	biological_process	DNA-templated transcription
G	0031011	cellular_component	Ino80 complex
G	0140658	molecular_function	ATP-dependent chromatin remodeler activity
H	0031011	cellular_component	Ino80 complex
I	0005634	cellular_component	nucleus
I	0006338	biological_process	chromatin remodeling
I	0031011	cellular_component	Ino80 complex
M	0000786	cellular_component	nucleosome
M	0003677	molecular_function	DNA binding
M	0005515	molecular_function	protein binding
M	0005576	cellular_component	extracellular region
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005694	cellular_component	chromosome
M	0006325	biological_process	chromatin organization
M	0006334	biological_process	nucleosome assembly
M	0030527	molecular_function	structural constituent of chromatin
M	0043229	cellular_component	intracellular organelle
M	0046982	molecular_function	protein heterodimerization activity
M	0070062	cellular_component	extracellular exosome
N	0000781	cellular_component	chromosome, telomeric region
N	0000786	cellular_component	nucleosome
N	0003677	molecular_function	DNA binding
N	0003723	molecular_function	RNA binding
N	0005515	molecular_function	protein binding
N	0005576	cellular_component	extracellular region
N	0005634	cellular_component	nucleus
N	0005654	cellular_component	nucleoplasm
N	0005694	cellular_component	chromosome
N	0006325	biological_process	chromatin organization
N	0006334	biological_process	nucleosome assembly
N	0016020	cellular_component	membrane
N	0030527	molecular_function	structural constituent of chromatin
N	0032200	biological_process	telomere organization
N	0032991	cellular_component	protein-containing complex
N	0043505	cellular_component	CENP-A containing nucleosome
N	0045653	biological_process	negative regulation of megakaryocyte differentiation
N	0046982	molecular_function	protein heterodimerization activity
N	0061644	biological_process	protein localization to CENP-A containing chromatin
N	0070062	cellular_component	extracellular exosome
O	0000786	cellular_component	nucleosome
O	0003677	molecular_function	DNA binding
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005694	cellular_component	chromosome
O	0008150	biological_process	biological_process
O	0019899	molecular_function	enzyme binding
O	0030527	molecular_function	structural constituent of chromatin
O	0031492	molecular_function	nucleosomal DNA binding
O	0031507	biological_process	heterochromatin formation
O	0043229	cellular_component	intracellular organelle
O	0046982	molecular_function	protein heterodimerization activity
O	0070062	cellular_component	extracellular exosome
P	0000786	cellular_component	nucleosome
P	0002227	biological_process	innate immune response in mucosa
P	0003677	molecular_function	DNA binding
P	0005515	molecular_function	protein binding
P	0005615	cellular_component	extracellular space
P	0005634	cellular_component	nucleus
P	0005654	cellular_component	nucleoplasm
P	0005694	cellular_component	chromosome
P	0005829	cellular_component	cytosol
P	0006334	biological_process	nucleosome assembly
P	0019731	biological_process	antibacterial humoral response
P	0030527	molecular_function	structural constituent of chromatin
P	0042742	biological_process	defense response to bacterium
P	0042802	molecular_function	identical protein binding
P	0043229	cellular_component	intracellular organelle
P	0046982	molecular_function	protein heterodimerization activity
P	0050830	biological_process	defense response to Gram-positive bacterium
P	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
P	0070062	cellular_component	extracellular exosome
Q	0000786	cellular_component	nucleosome
Q	0003677	molecular_function	DNA binding
Q	0005515	molecular_function	protein binding
Q	0005576	cellular_component	extracellular region
Q	0005634	cellular_component	nucleus
Q	0005654	cellular_component	nucleoplasm
Q	0005694	cellular_component	chromosome
Q	0006325	biological_process	chromatin organization
Q	0006334	biological_process	nucleosome assembly
Q	0030527	molecular_function	structural constituent of chromatin
Q	0043229	cellular_component	intracellular organelle
Q	0046982	molecular_function	protein heterodimerization activity
Q	0070062	cellular_component	extracellular exosome
R	0000781	cellular_component	chromosome, telomeric region
R	0000786	cellular_component	nucleosome
R	0003677	molecular_function	DNA binding
R	0003723	molecular_function	RNA binding
R	0005515	molecular_function	protein binding
R	0005576	cellular_component	extracellular region
R	0005634	cellular_component	nucleus
R	0005654	cellular_component	nucleoplasm
R	0005694	cellular_component	chromosome
R	0006325	biological_process	chromatin organization
R	0006334	biological_process	nucleosome assembly
R	0016020	cellular_component	membrane
R	0030527	molecular_function	structural constituent of chromatin
R	0032200	biological_process	telomere organization
R	0032991	cellular_component	protein-containing complex
R	0043505	cellular_component	CENP-A containing nucleosome
R	0045653	biological_process	negative regulation of megakaryocyte differentiation
R	0046982	molecular_function	protein heterodimerization activity
R	0061644	biological_process	protein localization to CENP-A containing chromatin
R	0070062	cellular_component	extracellular exosome
S	0000786	cellular_component	nucleosome
S	0003677	molecular_function	DNA binding
S	0005515	molecular_function	protein binding
S	0005634	cellular_component	nucleus
S	0005694	cellular_component	chromosome
S	0008150	biological_process	biological_process
S	0019899	molecular_function	enzyme binding
S	0030527	molecular_function	structural constituent of chromatin
S	0031492	molecular_function	nucleosomal DNA binding
S	0031507	biological_process	heterochromatin formation
S	0043229	cellular_component	intracellular organelle
S	0046982	molecular_function	protein heterodimerization activity
S	0070062	cellular_component	extracellular exosome
T	0000786	cellular_component	nucleosome
T	0002227	biological_process	innate immune response in mucosa
T	0003677	molecular_function	DNA binding
T	0005515	molecular_function	protein binding
T	0005615	cellular_component	extracellular space
T	0005634	cellular_component	nucleus
T	0005654	cellular_component	nucleoplasm
T	0005694	cellular_component	chromosome
T	0005829	cellular_component	cytosol
T	0006334	biological_process	nucleosome assembly
T	0019731	biological_process	antibacterial humoral response
T	0030527	molecular_function	structural constituent of chromatin
T	0042742	biological_process	defense response to bacterium
T	0042802	molecular_function	identical protein binding
T	0043229	cellular_component	intracellular organelle
T	0046982	molecular_function	protein heterodimerization activity
T	0050830	biological_process	defense response to Gram-positive bacterium
T	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
T	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	binding site for residue ADP A 501

Chain	Residue
A	ALA18
A	THR78
A	ALA79
A	TYR367
A	ILE375
A	ARG405
D	ARG313
A	HIS19
A	HIS21
A	PHE40
A	VAL41
A	PRO73
A	GLY74
A	GLY76
A	LYS77

---

site_id	AC2
Number of Residues	15
Details	binding site for residue ADP B 501

Chain	Residue
B	ALA18
B	HIS19
B	HIS21
B	GLY39
B	PHE40
B	VAL41
B	PRO73
B	THR75
B	GLY76
B	LYS77
B	THR78
B	TYR367
B	ARG405
E	ARG313
E	ARG352

---

site_id	AC3
Number of Residues	15
Details	binding site for residue ADP C 501

Chain	Residue
C	ALA18
C	HIS19
C	HIS21
C	GLY39
C	PHE40
C	VAL41
C	GLY72
C	GLY74
C	THR75
C	GLY76
C	LYS77
C	THR78
C	TYR367
C	ILE375
C	ARG405

---

site_id	AC4
Number of Residues	14
Details	binding site for residue ADP D 501

Chain	Residue
D	ALA23
D	HIS24
D	HIS26
D	GLY45
D	LEU46
D	VAL47
D	PRO79
D	SER80
D	GLY82
D	LYS83
D	THR84
D	ALA85
D	TYR361
D	ARG399

---

site_id	AC5
Number of Residues	15
Details	binding site for residue ADP E 501

Chain	Residue
E	ALA23
E	HIS24
E	HIS26
E	GLY45
E	LEU46
E	VAL47
E	PRO79
E	SER80
E	GLY82
E	LYS83
E	THR84
E	ALA85
E	TYR361
E	LEU398
E	ARG399

---

site_id	AC6
Number of Residues	15
Details	binding site for residue ADP F 501

Chain	Residue
F	ALA23
F	HIS24
F	HIS26
F	GLY45
F	LEU46
F	VAL47
F	PRO79
F	SER80
F	GLY82
F	LYS83
F	THR84
F	ALA85
F	TYR361
F	ILE369
F	ARG399

---

site_id	AC7
Number of Residues	12
Details	binding site for residue ATP J 801

Chain	Residue
J	LEU694
J	PHE695
J	GLY64
J	SER65
J	HIS66
J	ASP190
J	SER209
J	TYR210
J	SER211
J	GLU264
J	ARG268
J	GLY691

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
O	ALA21-VAL27

---

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

Chain	Residue	Details
N	GLY14-HIS18

---

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

Chain	Residue	Details
M	LYS14-LEU20

---

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

Chain	Residue	Details
P	ARG92-GLY114

---

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

Chain	Residue	Details
M	PRO66-ILE74

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: N-acetylproline => ECO:0000250|UniProtKB:P23527

Chain	Residue	Details
P	PRO1
T	PRO1

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: ADP-ribosyl glutamic acid => ECO:0000269|PubMed:27530147

Chain	Residue	Details
P	GLU2
T	GLU2

---

site_id	SWS_FT_FI3
Number of Residues	16
Details	MOD_RES: N6-lactoyllysine; alternate => ECO:0000269|PubMed:31645732

Chain	Residue	Details
P	LYS5
T	LYS11
T	LYS15
T	LYS16
T	LYS20
T	LYS23
T	LYS43
T	LYS85
P	LYS11
P	LYS15
P	LYS16
P	LYS20
P	LYS23
P	LYS43
P	LYS85
T	LYS5

---

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: ADP-ribosylserine => ECO:0000269|PubMed:34874266

Chain	Residue	Details
P	SER6
T	SER6
S	LYS9
S	LYS95

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: N6-crotonyllysine; alternate => ECO:0000269|PubMed:21925322

Chain	Residue	Details
P	LYS12
T	LYS12
N	LYS44
R	LYS8
R	LYS16
R	LYS44

---

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: Phosphoserine; by STK4/MST1 => ECO:0000269|PubMed:12757711

Chain	Residue	Details
P	SER14
T	SER14
N	LYS77
N	LYS91
R	LYS12
R	LYS31
R	LYS77
R	LYS91

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine => ECO:0000269|PubMed:24681537

Chain	Residue	Details
P	LYS24
T	LYS24

---

site_id	SWS_FT_FI8
Number of Residues	6
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435

Chain	Residue	Details
P	LYS34
P	LYS116
P	LYS120
T	LYS34
T	LYS116
T	LYS120

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: PolyADP-ribosyl glutamic acid => ECO:0000250|UniProtKB:Q64475

Chain	Residue	Details
P	GLU35
T	GLU35

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	MOD_RES: Phosphoserine; by AMPK => ECO:0000250|UniProtKB:Q6ZWY9

Chain	Residue	Details
P	SER36
T	SER36
Q	LYS14
Q	LYS56

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269|PubMed:16627869

Chain	Residue	Details
P	LYS46
P	LYS108
T	LYS46
T	LYS108

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: N6-(2-hydroxyisobutyryl)lysine; alternate => ECO:0000269|PubMed:24681537

Chain	Residue	Details
P	LYS57
T	LYS57

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	MOD_RES: Dimethylated arginine => ECO:0000250|UniProtKB:Q96A08

Chain	Residue	Details
P	ARG79
T	ARG79

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: Omega-N-methylarginine => ECO:0000250|UniProtKB:Q96A08

Chain	Residue	Details
P	ARG86
P	ARG92
T	ARG86
T	ARG92

---

site_id	SWS_FT_FI15
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q00729

Chain	Residue	Details
P	THR115
T	THR115
R	LYS91

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	CARBOHYD: O-linked (GlcNAc) serine => ECO:0000269|PubMed:22121020

Chain	Residue	Details
P	SER112
T	SER112
N	LYS79
R	LYS20
R	LYS59
R	LYS79

---

site_id	SWS_FT_FI17
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:P58876

Chain	Residue	Details
P	LYS5
T	LYS5

---

site_id	SWS_FT_FI18
Number of Residues	4
Details	CROSSLNK: 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

Chain	Residue	Details
M	SER57
P	LYS120
T	LYS120

---

site_id	SWS_FT_FI19
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2); alternate => ECO:0000250|UniProtKB:Q5QNW6

Chain	Residue	Details
P	LYS20
T	LYS20

---

site_id	SWS_FT_FI20
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate => ECO:0000269|PubMed:21726816

Chain	Residue	Details
P	LYS34
T	LYS34

---

site_id	SWS_FT_FI21
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243

Chain	Residue	Details
M	SER86
Q	SER86

---

site_id	SWS_FT_FI22
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332

Chain	Residue	Details
M	THR107
Q	THR107

---

site_id	SWS_FT_FI23
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297

Chain	Residue	Details
M	LYS115
Q	LYS115

---

site_id	SWS_FT_FI24
Number of Residues	2
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229

Chain	Residue	Details
M	LYS122
Q	LYS122

---

site_id	SWS_FT_FI25
Number of Residues	2
Details	LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806

Chain	Residue	Details
M	LYS18
Q	LYS18

---

site_id	SWS_FT_FI26
Number of Residues	2
Details	LIPID: S-palmitoyl cysteine => ECO:0000269|PubMed:21076176

Chain	Residue	Details
M	CYS110
Q	CYS110

---