Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4JJN

Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000500	cellular_component	RNA polymerase I upstream activating factor complex
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005694	cellular_component	chromosome
A	0006325	biological_process	chromatin organization
A	0006355	biological_process	regulation of DNA-templated transcription
A	0006878	biological_process	intracellular copper ion homeostasis
A	0008823	molecular_function	cupric reductase activity
A	0009060	biological_process	aerobic respiration
A	0009303	biological_process	rRNA transcription
A	0030527	molecular_function	structural constituent of chromatin
A	0031298	cellular_component	replication fork protection complex
A	0032991	cellular_component	protein-containing complex
A	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
A	0043505	cellular_component	CENP-A containing nucleosome
A	0043935	biological_process	sexual sporulation resulting in formation of a cellular spore
A	0045943	biological_process	positive regulation of transcription by RNA polymerase I
A	0046982	molecular_function	protein heterodimerization activity
A	0070911	biological_process	global genome nucleotide-excision repair
B	0000500	cellular_component	RNA polymerase I upstream activating factor complex
B	0000786	cellular_component	nucleosome
B	0003677	molecular_function	DNA binding
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005694	cellular_component	chromosome
B	0006325	biological_process	chromatin organization
B	0006334	biological_process	nucleosome assembly
B	0006355	biological_process	regulation of DNA-templated transcription
B	0030527	molecular_function	structural constituent of chromatin
B	0031298	cellular_component	replication fork protection complex
B	0032991	cellular_component	protein-containing complex
B	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
B	0045943	biological_process	positive regulation of transcription by RNA polymerase I
B	0046982	molecular_function	protein heterodimerization activity
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
C	0006281	biological_process	DNA repair
C	0006325	biological_process	chromatin organization
C	0030527	molecular_function	structural constituent of chromatin
C	0031298	cellular_component	replication fork protection complex
C	0031492	molecular_function	nucleosomal DNA binding
C	0031507	biological_process	heterochromatin formation
C	0032991	cellular_component	protein-containing complex
C	0046982	molecular_function	protein heterodimerization activity
D	0000786	cellular_component	nucleosome
D	0003677	molecular_function	DNA binding
D	0005515	molecular_function	protein binding
D	0005634	cellular_component	nucleus
D	0005694	cellular_component	chromosome
D	0006325	biological_process	chromatin organization
D	0006355	biological_process	regulation of DNA-templated transcription
D	0030527	molecular_function	structural constituent of chromatin
D	0031298	cellular_component	replication fork protection complex
D	0032991	cellular_component	protein-containing complex
D	0046982	molecular_function	protein heterodimerization activity
E	0000500	cellular_component	RNA polymerase I upstream activating factor complex
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0005515	molecular_function	protein binding
E	0005634	cellular_component	nucleus
E	0005694	cellular_component	chromosome
E	0006325	biological_process	chromatin organization
E	0006355	biological_process	regulation of DNA-templated transcription
E	0006878	biological_process	intracellular copper ion homeostasis
E	0008823	molecular_function	cupric reductase activity
E	0009060	biological_process	aerobic respiration
E	0009303	biological_process	rRNA transcription
E	0030527	molecular_function	structural constituent of chromatin
E	0031298	cellular_component	replication fork protection complex
E	0032991	cellular_component	protein-containing complex
E	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
E	0043505	cellular_component	CENP-A containing nucleosome
E	0043935	biological_process	sexual sporulation resulting in formation of a cellular spore
E	0045943	biological_process	positive regulation of transcription by RNA polymerase I
E	0046982	molecular_function	protein heterodimerization activity
E	0070911	biological_process	global genome nucleotide-excision repair
F	0000500	cellular_component	RNA polymerase I upstream activating factor complex
F	0000786	cellular_component	nucleosome
F	0003677	molecular_function	DNA binding
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005694	cellular_component	chromosome
F	0006325	biological_process	chromatin organization
F	0006334	biological_process	nucleosome assembly
F	0006355	biological_process	regulation of DNA-templated transcription
F	0030527	molecular_function	structural constituent of chromatin
F	0031298	cellular_component	replication fork protection complex
F	0032991	cellular_component	protein-containing complex
F	0042790	biological_process	nucleolar large rRNA transcription by RNA polymerase I
F	0045943	biological_process	positive regulation of transcription by RNA polymerase I
F	0046982	molecular_function	protein heterodimerization activity
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005634	cellular_component	nucleus
G	0005694	cellular_component	chromosome
G	0006281	biological_process	DNA repair
G	0006325	biological_process	chromatin organization
G	0030527	molecular_function	structural constituent of chromatin
G	0031298	cellular_component	replication fork protection complex
G	0031492	molecular_function	nucleosomal DNA binding
G	0031507	biological_process	heterochromatin formation
G	0032991	cellular_component	protein-containing complex
G	0046982	molecular_function	protein heterodimerization activity
H	0000786	cellular_component	nucleosome
H	0003677	molecular_function	DNA binding
H	0005515	molecular_function	protein binding
H	0005634	cellular_component	nucleus
H	0005694	cellular_component	chromosome
H	0006325	biological_process	chromatin organization
H	0006355	biological_process	regulation of DNA-templated transcription
H	0030527	molecular_function	structural constituent of chromatin
H	0031298	cellular_component	replication fork protection complex
H	0032991	cellular_component	protein-containing complex
H	0046982	molecular_function	protein heterodimerization activity
K	0003682	molecular_function	chromatin binding
L	0003682	molecular_function	chromatin binding

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	LYS14-LEU20

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

Chain	Residue	Details
A	PRO66-ILE74

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

Chain	Residue	Details
D	ARG95-GLY117

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

Chain	Residue	Details
B	GLY14-HIS18

site_id	PS00014
Number of Residues	4
Details	ER_TARGET Endoplasmic reticulum targeting sequence. SQEL

Chain	Residue	Details
C	SER128-LEU131

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

Chain	Residue	Details
C	ALA22-VAL28

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: N-acetylalanine => ECO:0000269\|PubMed:15454564

Chain	Residue	Details
H	LYS6
H	LYS7
K	ALA2
L	ALA2

site_id	SWS_FT_FI2
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0000269\|PubMed:15652479, ECO:0000269\|PubMed:15970663

Chain	Residue	Details
F	LYS5
F	LYS8
F	LYS12
D	SER10
H	SER10
B	LYS12

site_id	SWS_FT_FI3
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:11545749, ECO:0000269\|PubMed:15186774

Chain	Residue	Details
D	LYS11
H	LYS11

site_id	SWS_FT_FI4
Number of Residues	2
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0000269\|PubMed:11545749, ECO:0000269\|PubMed:15186774, ECO:0000269\|PubMed:16598039, ECO:0000269\|PubMed:19113941

Chain	Residue	Details
H	LYS16
F	LYS31
F	LYS77
D	LYS16

site_id	SWS_FT_FI5
Number of Residues	2
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0000269\|PubMed:19113941

Chain	Residue	Details
G	LYS13
G	LYS21
H	LYS17
D	LYS17

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N6-butyryllysine; alternate => ECO:0000269\|PubMed:19113941

Chain	Residue	Details
H	LYS21
D	LYS21

site_id	SWS_FT_FI7
Number of Residues	2
Details	MOD_RES: N6-methyllysine; alternate => ECO:0000269\|PubMed:19113941

Chain	Residue	Details
D	LYS22
H	LYS22

site_id	SWS_FT_FI8
Number of Residues	4
Details	MOD_RES: N6-succinyllysine => ECO:0000269\|PubMed:22389435

Chain	Residue	Details
D	LYS34
D	LYS46
H	LYS34
H	LYS46

site_id	SWS_FT_FI9
Number of Residues	2
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000269\|PubMed:19113941

Chain	Residue	Details
D	LYS37
G	LYS126
H	LYS37

site_id	SWS_FT_FI10
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate

Chain	Residue	Details
D	LYS6
D	LYS7
H	LYS6
H	LYS7

site_id	SWS_FT_FI11
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:12535538, ECO:0000269\|PubMed:12535539, ECO:0000269\|PubMed:14660635, ECO:0000269\|PubMed:15280549

Chain	Residue	Details
D	LYS123
H	LYS123

site_id	SWS_FT_FI12
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO); alternate => ECO:0000305

Chain	Residue	Details
D	LYS16
D	LYS17
H	LYS16
H	LYS17

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)