Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1EQZ

X-RAY STRUCTURE OF THE NUCLEOSOME CORE PARTICLE AT 2.5 A RESOLUTION

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000786	cellular_component	nucleosome
A	0003677	molecular_function	DNA binding
A	0005634	cellular_component	nucleus
A	0005694	cellular_component	chromosome
A	0030527	molecular_function	structural constituent of chromatin
A	0031507	biological_process	heterochromatin formation
A	0046982	molecular_function	protein heterodimerization activity
B	0000786	cellular_component	nucleosome
B	0002227	biological_process	innate immune response in mucosa
B	0003677	molecular_function	DNA binding
B	0005615	cellular_component	extracellular space
B	0005634	cellular_component	nucleus
B	0005694	cellular_component	chromosome
B	0006325	biological_process	chromatin organization
B	0019731	biological_process	antibacterial humoral response
B	0030527	molecular_function	structural constituent of chromatin
B	0044877	molecular_function	protein-containing complex binding
B	0046982	molecular_function	protein heterodimerization activity
B	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
C	0000786	cellular_component	nucleosome
C	0003677	molecular_function	DNA binding
C	0005634	cellular_component	nucleus
C	0005694	cellular_component	chromosome
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
D	0000786	cellular_component	nucleosome
D	0003677	molecular_function	DNA binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005694	cellular_component	chromosome
D	0006334	biological_process	nucleosome assembly
D	0030527	molecular_function	structural constituent of chromatin
D	0046982	molecular_function	protein heterodimerization activity
E	0000786	cellular_component	nucleosome
E	0003677	molecular_function	DNA binding
E	0005634	cellular_component	nucleus
E	0005694	cellular_component	chromosome
E	0030527	molecular_function	structural constituent of chromatin
E	0031507	biological_process	heterochromatin formation
E	0046982	molecular_function	protein heterodimerization activity
F	0000786	cellular_component	nucleosome
F	0002227	biological_process	innate immune response in mucosa
F	0003677	molecular_function	DNA binding
F	0005615	cellular_component	extracellular space
F	0005634	cellular_component	nucleus
F	0005694	cellular_component	chromosome
F	0006325	biological_process	chromatin organization
F	0019731	biological_process	antibacterial humoral response
F	0030527	molecular_function	structural constituent of chromatin
F	0044877	molecular_function	protein-containing complex binding
F	0046982	molecular_function	protein heterodimerization activity
F	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
G	0000786	cellular_component	nucleosome
G	0003677	molecular_function	DNA binding
G	0005634	cellular_component	nucleus
G	0005694	cellular_component	chromosome
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
H	0000786	cellular_component	nucleosome
H	0003677	molecular_function	DNA binding
H	0005634	cellular_component	nucleus
H	0005654	cellular_component	nucleoplasm
H	0005694	cellular_component	chromosome
H	0006334	biological_process	nucleosome assembly
H	0030527	molecular_function	structural constituent of chromatin
H	0046982	molecular_function	protein heterodimerization activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL A 449

Chain	Residue
A	GLY44
A	GLY46
A	ALA47
B	THR90
B	SER91

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL E 450

Chain	Residue
F	SER91
E	GLY44
E	GLY46
E	ALA47
F	THR90

site_id	AC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE CAC G 451

Chain	Residue
A	GLU64
B	GLN47
B	VAL48
B	HIS49
G	GLU73
G	GLN76
G	ASP77
H	LEU22

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE K J 452

Chain	Residue
J	DA255
J	DA256

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE K J 453

Chain	Residue
A	LYS124
J	DG216

site_id	AC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE K J 454

Chain	Residue
J	DG217

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE K J 455

Chain	Residue
J	DG227

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE K J 456

Chain	Residue
J	DA228

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE K J 457

Chain	Residue
J	DA175

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE K I 458

Chain	Residue
I	DG97
I	DG98

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN J 459

Chain	Residue
J	DG280
J	HOH500
J	HOH507

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 460

Chain	Residue
I	DG134
I	HOH505

site_id	BC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 461

Chain	Residue
I	HOH509

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN J 462

Chain	Residue
I	DT140
I	HOH511
J	DG246

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 463

Chain	Residue
I	DG121
I	HOH513

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 464

Chain	Residue
I	DG70
I	DG71

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN I 465

Chain	Residue
I	DG39
I	DG40
I	HOH514

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE MN I 466

Chain	Residue
I	DG137
I	DG138
I	HOH488

site_id	CC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 467

Chain	Residue
J	DG185
J	DG186

site_id	CC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN J 468

Chain	Residue
J	DG267
J	HOH503

site_id	CC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN J 469

Chain	Residue
J	DA147

site_id	CC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 470

Chain	Residue
I	DG100

site_id	CC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE MN I 471

Chain	Residue
I	DA1

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 472

Chain	Residue
I	DA17
I	DG18

site_id	CC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE MN I 473

Chain	Residue
I	DA124
I	DG125

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ALA21-VAL27

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

Chain	Residue	Details
D	GLY14-HIS18

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

Chain	Residue	Details
C	LYS14-LEU20

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

Chain	Residue	Details
B	ARG92-GLY114

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

Chain	Residue	Details
C	PRO66-ILE74

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	24
Details	Compositional bias: {"description":"Basic residues","evidences":[{"source":"SAM","id":"MobiDB-lite","evidenceCode":"ECO:0000256"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"12450536","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"N6-(2-hydroxyisobutyryl)lysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	8
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"2713375","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"12865423","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	2
Details	Glycosylation: {"description":"O-linked (GlcNAc) serine","evidences":[{"source":"UniProtKB","id":"P62807","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	2
Details	Site: {"description":"Involved in HMGB1-binding"}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	3
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"PubMed","id":"12123664","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P84228","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	4
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	2
Details	Lipidation: {"description":"S-palmitoyl cysteine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	1
Details	Modified residue: {"description":"Citrulline; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI27
Number of Residues	1
Details	Modified residue: {"description":"Citrulline","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI28
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI29
Number of Residues	8
Details	DNA binding: {}

Chain

Residue

Details

site_id	SWS_FT_FI30
Number of Residues	7
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI31
Number of Residues	3
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI32
Number of Residues	4
Details	Modified residue: {"description":"N6-succinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI33
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine; by PAK2","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI34
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI35
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI36
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI37
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in UFM1); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI38
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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