Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8OX1

Structure of TRF1core in complex with telomeric nucleosome

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	0045296	molecular_function	cadherin binding
A	0046982	molecular_function	protein heterodimerization activity
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	0046982	molecular_function	protein heterodimerization activity
B	0061644	biological_process	protein localization to CENP-A containing chromatin
B	0070062	cellular_component	extracellular exosome
C	0000786	cellular_component	nucleosome
C	0003674	molecular_function	molecular_function
C	0003677	molecular_function	DNA binding
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005694	cellular_component	chromosome
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	0046982	molecular_function	protein heterodimerization activity
C	0070062	cellular_component	extracellular exosome
D	0000786	cellular_component	nucleosome
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	0006334	biological_process	nucleosome assembly
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0042742	biological_process	defense response to bacterium
D	0042802	molecular_function	identical protein binding
D	0046982	molecular_function	protein heterodimerization activity
D	0050830	biological_process	defense response to Gram-positive bacterium
D	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
D	0070062	cellular_component	extracellular exosome
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	0045296	molecular_function	cadherin binding
E	0046982	molecular_function	protein heterodimerization activity
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	0046982	molecular_function	protein heterodimerization activity
F	0061644	biological_process	protein localization to CENP-A containing chromatin
F	0070062	cellular_component	extracellular exosome
G	0000786	cellular_component	nucleosome
G	0003674	molecular_function	molecular_function
G	0003677	molecular_function	DNA binding
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005654	cellular_component	nucleoplasm
G	0005694	cellular_component	chromosome
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	0046982	molecular_function	protein heterodimerization activity
G	0070062	cellular_component	extracellular exosome
H	0000786	cellular_component	nucleosome
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	0006334	biological_process	nucleosome assembly
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0042742	biological_process	defense response to bacterium
H	0042802	molecular_function	identical protein binding
H	0046982	molecular_function	protein heterodimerization activity
H	0050830	biological_process	defense response to Gram-positive bacterium
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
H	0070062	cellular_component	extracellular exosome
L	0000723	biological_process	telomere maintenance
L	0000781	cellular_component	chromosome, telomeric region
L	0000783	cellular_component	nuclear telomere cap complex
L	0001650	cellular_component	fibrillar center
L	0003677	molecular_function	DNA binding
L	0003691	molecular_function	double-stranded telomeric DNA binding
L	0003720	molecular_function	telomerase activity
L	0005515	molecular_function	protein binding
L	0005634	cellular_component	nucleus
L	0005654	cellular_component	nucleoplasm
L	0005694	cellular_component	chromosome
L	0005730	cellular_component	nucleolus
L	0005737	cellular_component	cytoplasm
L	0005819	cellular_component	spindle
L	0005856	cellular_component	cytoskeleton
L	0007004	biological_process	telomere maintenance via telomerase
L	0008017	molecular_function	microtubule binding
L	0008156	biological_process	negative regulation of DNA replication
L	0008301	molecular_function	DNA binding, bending
L	0016233	biological_process	telomere capping
L	0016604	cellular_component	nuclear body
L	0032206	biological_process	positive regulation of telomere maintenance
L	0032211	biological_process	negative regulation of telomere maintenance via telomerase
L	0032214	biological_process	negative regulation of telomere maintenance via semi-conservative replication
L	0042162	molecular_function	telomeric DNA binding
L	0042802	molecular_function	identical protein binding
L	0042803	molecular_function	protein homodimerization activity
L	0045141	biological_process	meiotic telomere clustering
L	0051301	biological_process	cell division
L	0061820	biological_process	telomeric D-loop disassembly
L	0070187	cellular_component	shelterin complex
L	0071532	molecular_function	ankyrin repeat binding
L	0090656	biological_process	t-circle formation
L	0098505	molecular_function	G-rich strand telomeric DNA binding
L	1904357	biological_process	negative regulation of telomere maintenance via telomere lengthening
L	1904792	biological_process	positive regulation of shelterin complex assembly
L	1904850	biological_process	negative regulation of establishment of protein localization to telomere
L	1904911	biological_process	negative regulation of establishment of RNA localization to telomere
L	1904914	biological_process	negative regulation of establishment of protein-containing complex localization to telomere
L	1905778	biological_process	negative regulation of exonuclease activity
L	1905839	biological_process	negative regulation of telomeric D-loop disassembly
M	0000723	biological_process	telomere maintenance
M	0000781	cellular_component	chromosome, telomeric region
M	0000783	cellular_component	nuclear telomere cap complex
M	0001650	cellular_component	fibrillar center
M	0003677	molecular_function	DNA binding
M	0003691	molecular_function	double-stranded telomeric DNA binding
M	0003720	molecular_function	telomerase activity
M	0005515	molecular_function	protein binding
M	0005634	cellular_component	nucleus
M	0005654	cellular_component	nucleoplasm
M	0005694	cellular_component	chromosome
M	0005730	cellular_component	nucleolus
M	0005737	cellular_component	cytoplasm
M	0005819	cellular_component	spindle
M	0005856	cellular_component	cytoskeleton
M	0007004	biological_process	telomere maintenance via telomerase
M	0008017	molecular_function	microtubule binding
M	0008156	biological_process	negative regulation of DNA replication
M	0008301	molecular_function	DNA binding, bending
M	0016233	biological_process	telomere capping
M	0016604	cellular_component	nuclear body
M	0032206	biological_process	positive regulation of telomere maintenance
M	0032211	biological_process	negative regulation of telomere maintenance via telomerase
M	0032214	biological_process	negative regulation of telomere maintenance via semi-conservative replication
M	0042162	molecular_function	telomeric DNA binding
M	0042802	molecular_function	identical protein binding
M	0042803	molecular_function	protein homodimerization activity
M	0045141	biological_process	meiotic telomere clustering
M	0051301	biological_process	cell division
M	0061820	biological_process	telomeric D-loop disassembly
M	0070187	cellular_component	shelterin complex
M	0071532	molecular_function	ankyrin repeat binding
M	0090656	biological_process	t-circle formation
M	0098505	molecular_function	G-rich strand telomeric DNA binding
M	1904357	biological_process	negative regulation of telomere maintenance via telomere lengthening
M	1904792	biological_process	positive regulation of shelterin complex assembly
M	1904850	biological_process	negative regulation of establishment of protein localization to telomere
M	1904911	biological_process	negative regulation of establishment of RNA localization to telomere
M	1904914	biological_process	negative regulation of establishment of protein-containing complex localization to telomere
M	1905778	biological_process	negative regulation of exonuclease activity
M	1905839	biological_process	negative regulation of telomeric D-loop disassembly

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
C	ALA21-VAL27

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. REIQTavRlLLpGELaKHAVSEG

Chain	Residue	Details
D	ARG89-GLY111

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	25
Details	DNA_BIND: H-T-H motif => ECO:0000255\|PROSITE-ProRule:PRU00625

Chain	Residue	Details
M	TRP403-LYS428
H	PRO-2

site_id	SWS_FT_FI2
Number of Residues	1
Details	MOD_RES: N-acetylalanine => ECO:0007744\|PubMed:19413330, ECO:0007744\|PubMed:20068231

Chain	Residue	Details
M	ALA2
H	GLU-1

site_id	SWS_FT_FI3
Number of Residues	1
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:17081983, ECO:0007744\|PubMed:20068231, ECO:0007744\|PubMed:23186163

Chain	Residue	Details
M	SER11
H	LYS8
H	LYS12
H	LYS13
H	LYS17
H	LYS20
H	LYS40
H	LYS82
D	LYS8
D	LYS12
D	LYS13
D	LYS17
D	LYS20
D	LYS40
D	LYS82
H	LYS2

site_id	SWS_FT_FI4
Number of Residues	1
Details	MOD_RES: Phosphoserine; by ATM => ECO:0000269\|PubMed:11375976

Chain	Residue	Details
M	SER219
H	SER3
G	LYS9
G	LYS95

site_id	SWS_FT_FI5
Number of Residues	4
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744\|PubMed:28112733

Chain	Residue	Details
M	LYS213
H	LYS9
M	LYS325
M	LYS366
F	LYS16
F	LYS44

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

Chain	Residue	Details
D	SER11
H	SER11
B	LYS77
B	LYS91
F	LYS12
F	LYS31
F	LYS77
F	LYS91

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

Chain	Residue	Details
D	LYS21
H	LYS21
G	LYS74
G	LYS75

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

Chain	Residue	Details
D	LYS31
D	LYS113
D	LYS117
H	LYS31
H	LYS113
H	LYS117

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

Chain	Residue	Details
D	GLU32
H	GLU32
C	LYS125
G	LYS118
G	LYS119
G	LYS125

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

Chain	Residue	Details
D	SER33
H	SER33
E	LYS14
E	LYS56

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

Chain	Residue	Details
D	LYS43
D	LYS105
H	LYS43
H	LYS105

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	LYS54
H	LYS54
E	LYS18
G	LYS119

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

Chain	Residue	Details
D	ARG76
H	ARG76

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

Chain	Residue	Details
D	ARG83
D	ARG89
H	ARG83
H	ARG89

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

Chain	Residue	Details
D	THR112
H	THR112
F	LYS91

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

Chain	Residue	Details
D	SER109
H	SER109
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	LYS2
H	LYS2

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
A	LYS37
D	LYS117
H	LYS117

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	LYS17
H	LYS17

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	LYS31
H	LYS31

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

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