8SN7

Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 5)

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	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0006325	biological_process	chromatin organization
A	0006334	biological_process	nucleosome assembly
A	0010467	biological_process	gene expression
A	0016020	cellular_component	membrane
A	0030527	molecular_function	structural constituent of chromatin
A	0032200	biological_process	telomere organization
A	0032991	cellular_component	protein-containing complex
A	0040029	biological_process	epigenetic regulation of gene expression
A	0043229	cellular_component	intracellular organelle
A	0045296	molecular_function	cadherin binding
A	0070062	cellular_component	extracellular exosome
B	0000781	cellular_component	chromosome, telomeric region
B	0000786	cellular_component	nucleosome
B	0003677	molecular_function	DNA binding
B	0003723	molecular_function	RNA binding
B	0005515	molecular_function	protein binding
B	0005576	cellular_component	extracellular region
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005694	cellular_component	chromosome
B	0006325	biological_process	chromatin organization
B	0006334	biological_process	nucleosome assembly
B	0016020	cellular_component	membrane
B	0030527	molecular_function	structural constituent of chromatin
B	0032200	biological_process	telomere organization
B	0032991	cellular_component	protein-containing complex
B	0043505	cellular_component	CENP-A containing nucleosome
B	0045653	biological_process	negative regulation of megakaryocyte differentiation
B	0061644	biological_process	protein localization to CENP-A containing chromatin
B	0070062	cellular_component	extracellular exosome
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	0006325	biological_process	chromatin organization
C	0008285	biological_process	negative regulation of cell population proliferation
C	0030527	molecular_function	structural constituent of chromatin
C	0031492	molecular_function	nucleosomal DNA binding
C	0031507	biological_process	heterochromatin formation
C	0043229	cellular_component	intracellular organelle
C	0043505	cellular_component	CENP-A containing nucleosome
C	0046982	molecular_function	protein heterodimerization activity
C	0061644	biological_process	protein localization to CENP-A containing chromatin
C	0070062	cellular_component	extracellular exosome
D	0000786	cellular_component	nucleosome
D	0001530	molecular_function	lipopolysaccharide binding
D	0002227	biological_process	innate immune response in mucosa
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005615	cellular_component	extracellular space
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005694	cellular_component	chromosome
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006325	biological_process	chromatin organization
D	0006334	biological_process	nucleosome assembly
D	0010804	biological_process	negative regulation of tumor necrosis factor-mediated signaling pathway
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0031640	biological_process	killing of cells of another organism
D	0042742	biological_process	defense response to bacterium
D	0043229	cellular_component	intracellular organelle
D	0043505	cellular_component	CENP-A containing nucleosome
D	0046982	molecular_function	protein heterodimerization activity
D	0050829	biological_process	defense response to Gram-negative bacterium
D	0050830	biological_process	defense response to Gram-positive bacterium
D	0061644	biological_process	protein localization to CENP-A containing chromatin
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
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	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0006325	biological_process	chromatin organization
E	0006334	biological_process	nucleosome assembly
E	0010467	biological_process	gene expression
E	0016020	cellular_component	membrane
E	0030527	molecular_function	structural constituent of chromatin
E	0032200	biological_process	telomere organization
E	0032991	cellular_component	protein-containing complex
E	0040029	biological_process	epigenetic regulation of gene expression
E	0043229	cellular_component	intracellular organelle
E	0045296	molecular_function	cadherin binding
E	0070062	cellular_component	extracellular exosome
F	0000781	cellular_component	chromosome, telomeric region
F	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0003723	molecular_function	RNA binding
F	0005515	molecular_function	protein binding
F	0005576	cellular_component	extracellular region
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005694	cellular_component	chromosome
F	0006325	biological_process	chromatin organization
F	0006334	biological_process	nucleosome assembly
F	0016020	cellular_component	membrane
F	0030527	molecular_function	structural constituent of chromatin
F	0032200	biological_process	telomere organization
F	0032991	cellular_component	protein-containing complex
F	0043505	cellular_component	CENP-A containing nucleosome
F	0045653	biological_process	negative regulation of megakaryocyte differentiation
F	0061644	biological_process	protein localization to CENP-A containing chromatin
F	0070062	cellular_component	extracellular exosome
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	0006325	biological_process	chromatin organization
G	0008285	biological_process	negative regulation of cell population proliferation
G	0030527	molecular_function	structural constituent of chromatin
G	0031492	molecular_function	nucleosomal DNA binding
G	0031507	biological_process	heterochromatin formation
G	0043229	cellular_component	intracellular organelle
G	0043505	cellular_component	CENP-A containing nucleosome
G	0046982	molecular_function	protein heterodimerization activity
G	0061644	biological_process	protein localization to CENP-A containing chromatin
G	0070062	cellular_component	extracellular exosome
H	0000786	cellular_component	nucleosome
H	0001530	molecular_function	lipopolysaccharide binding
H	0002227	biological_process	innate immune response in mucosa
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005615	cellular_component	extracellular space
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005694	cellular_component	chromosome
H	0005829	cellular_component	cytosol
H	0005886	cellular_component	plasma membrane
H	0006325	biological_process	chromatin organization
H	0006334	biological_process	nucleosome assembly
H	0010804	biological_process	negative regulation of tumor necrosis factor-mediated signaling pathway
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0031640	biological_process	killing of cells of another organism
H	0042742	biological_process	defense response to bacterium
H	0043229	cellular_component	intracellular organelle
H	0043505	cellular_component	CENP-A containing nucleosome
H	0046982	molecular_function	protein heterodimerization activity
H	0050829	biological_process	defense response to Gram-negative bacterium
H	0050830	biological_process	defense response to Gram-positive bacterium
H	0061644	biological_process	protein localization to CENP-A containing chromatin
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
L	0000122	biological_process	negative regulation of transcription by RNA polymerase II
L	0000151	cellular_component	ubiquitin ligase complex
L	0000209	biological_process	protein polyubiquitination
L	0004842	molecular_function	ubiquitin-protein transferase activity
L	0005515	molecular_function	protein binding
L	0005524	molecular_function	ATP binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005768	cellular_component	endosome
L	0005829	cellular_component	cytosol
L	0005886	cellular_component	plasma membrane
L	0006281	biological_process	DNA repair
L	0006511	biological_process	ubiquitin-dependent protein catabolic process
L	0006513	biological_process	protein monoubiquitination
L	0006915	biological_process	apoptotic process
L	0010008	cellular_component	endosome membrane
L	0016567	biological_process	protein ubiquitination
L	0016740	molecular_function	transferase activity
L	0019787	molecular_function	ubiquitin-like protein transferase activity
L	0030514	biological_process	negative regulation of BMP signaling pathway
L	0031625	molecular_function	ubiquitin protein ligase binding
L	0036211	biological_process	protein modification process
L	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
L	0051865	biological_process	protein autoubiquitination
L	0061630	molecular_function	ubiquitin protein ligase activity
L	0061631	molecular_function	ubiquitin conjugating enzyme activity
L	0070062	cellular_component	extracellular exosome
L	0070936	biological_process	protein K48-linked ubiquitination
L	0070979	biological_process	protein K11-linked ubiquitination
L	0085020	biological_process	protein K6-linked ubiquitination
L	1903955	biological_process	positive regulation of protein targeting to mitochondrion

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	ALA134-VAL140

---

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

Chain	Residue	Details
B	GLY14-HIS18

---

site_id	PS00183
Number of Residues	16
Details	UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInsn.GsICLdiL

Chain	Residue	Details
L	TYR74-LEU89

---

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KakIqDkegIPpdqQrLIFaGkqleD

Chain	Residue	Details
M	LYS27-ASP52

---

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. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
D	ARG92-GLY114

---

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	SITE: Interacts with activating enzyme

Chain	Residue	Details
M	ARG54
M	ARG72

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	SITE: Essential for function

Chain	Residue	Details
M	HIS68
H	GLU2

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphoserine; by PINK1 => ECO:0000269|PubMed:24660806, ECO:0000269|PubMed:24751536, ECO:0000269|PubMed:24784582, ECO:0000269|PubMed:25527291

Chain	Residue	Details
M	SER65
H	LYS11
H	LYS15
H	LYS16
H	LYS20
H	LYS23
H	LYS43
H	LYS85
D	LYS11
D	LYS15
D	LYS16
D	LYS20
D	LYS23
D	LYS43
D	LYS85
H	LYS5

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: (Microbial infection) ADP-ribosylthreonine => ECO:0000269|PubMed:32330457

Chain	Residue	Details
M	THR66
H	SER6

---

site_id	SWS_FT_FI5
Number of Residues	1
Details	MOD_RES: ADP-ribosylglycine => ECO:0000269|PubMed:28525742

Chain	Residue	Details
M	GLY76
H	LYS12
B	LYS44
F	LYS8
F	LYS16
F	LYS44

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000305|PubMed:15466860

Chain	Residue	Details
M	LYS27
H	SER14
C	LYS238
G	LYS5
G	LYS6
G	LYS12
F	LYS77
F	LYS91

---

site_id	SWS_FT_FI7
Number of Residues	2
Details	CROSSLNK: Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)

Chain	Residue	Details
D	LYS24
M	GLY76

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:25752573, ECO:0000269|PubMed:25752577, ECO:0000269|PubMed:34239127

Chain	Residue	Details
M	LYS29
D	LYS116
D	LYS120
H	LYS34
H	LYS116
H	LYS120

---

site_id	SWS_FT_FI9
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:25752577

Chain	Residue	Details
M	LYS33
H	GLU35
G	LYS6

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16443603, ECO:0000269|PubMed:16543144

Chain	Residue	Details
M	LYS48
H	SER36
E	LYS14
E	LYS56

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269|PubMed:16543144, ECO:0000269|PubMed:18719106

Chain	Residue	Details
M	LYS63
D	LYS108
H	LYS46
H	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
D	LYS57
H	LYS57
E	LYS18
E	LYS64

---

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

Chain	Residue	Details
D	ARG79
H	ARG79

---

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

Chain	Residue	Details
D	ARG86
D	ARG92
H	ARG86
H	ARG92

---

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

Chain	Residue	Details
D	THR115
H	THR115
F	LYS91

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	CARBOHYD: O-linked (GlcNAc) serine => ECO:0000250|UniProtKB:P62807

Chain	Residue	Details
D	SER112
H	SER112
B	LYS79
F	LYS20
F	LYS59
F	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
D	LYS5
H	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

Chain	Residue	Details
A	LYS37
D	LYS120
H	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
D	LYS20
H	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
D	LYS34
H	LYS34

---

site_id	SWS_FT_FI21
Number of Residues	2
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:29211711

Chain	Residue	Details
A	LYS79
E	LYS79

---

site_id	SWS_FT_FI22
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:20850016

Chain	Residue	Details
A	THR80
E	THR80

---

site_id	SWS_FT_FI23
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P84243

Chain	Residue	Details
A	SER86
E	SER86

---

site_id	SWS_FT_FI24
Number of Residues	2
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:Q71DI3

Chain	Residue	Details
A	THR107
E	THR107

---

site_id	SWS_FT_FI25
Number of Residues	2
Details	MOD_RES: N6-glutaryllysine; alternate => ECO:0000269|PubMed:31542297

Chain	Residue	Details
A	LYS115
E	LYS115

---

site_id	SWS_FT_FI26
Number of Residues	2
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000269|PubMed:22389435, ECO:0000269|PubMed:27436229

Chain	Residue	Details
A	LYS122
E	LYS122

---

site_id	SWS_FT_FI27
Number of Residues	2
Details	LIPID: N6-decanoyllysine => ECO:0000269|PubMed:35939806

Chain	Residue	Details
A	LYS18
E	LYS18

---