Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

9CG9

Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2

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	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005694	cellular_component	chromosome
A	0030527	molecular_function	structural constituent of chromatin
A	0031492	molecular_function	nucleosomal DNA binding
A	0031507	biological_process	heterochromatin formation
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	0006334	biological_process	nucleosome assembly
B	0030527	molecular_function	structural constituent of chromatin
B	0031507	biological_process	heterochromatin formation
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	0031507	biological_process	heterochromatin formation
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	0005694	cellular_component	chromosome
D	0006325	biological_process	chromatin organization
D	0019731	biological_process	antibacterial humoral response
D	0030527	molecular_function	structural constituent of chromatin
D	0031507	biological_process	heterochromatin formation
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	0005634	cellular_component	nucleus
E	0005654	cellular_component	nucleoplasm
E	0005694	cellular_component	chromosome
E	0030527	molecular_function	structural constituent of chromatin
E	0031492	molecular_function	nucleosomal DNA binding
E	0031507	biological_process	heterochromatin formation
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	0006334	biological_process	nucleosome assembly
F	0030527	molecular_function	structural constituent of chromatin
F	0031507	biological_process	heterochromatin formation
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	0031507	biological_process	heterochromatin formation
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	0005694	cellular_component	chromosome
H	0006325	biological_process	chromatin organization
H	0019731	biological_process	antibacterial humoral response
H	0030527	molecular_function	structural constituent of chromatin
H	0031507	biological_process	heterochromatin formation
H	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
K	0000122	biological_process	negative regulation of transcription by RNA polymerase II
K	0000400	molecular_function	four-way junction DNA binding
K	0000405	molecular_function	bubble DNA binding
K	0000793	cellular_component	condensed chromosome
K	0000976	molecular_function	transcription cis-regulatory region binding
K	0001530	molecular_function	lipopolysaccharide binding
K	0001773	biological_process	myeloid dendritic cell activation
K	0001786	molecular_function	phosphatidylserine binding
K	0001935	biological_process	endothelial cell proliferation
K	0001938	biological_process	positive regulation of endothelial cell proliferation
K	0002218	biological_process	activation of innate immune response
K	0002250	biological_process	adaptive immune response
K	0002270	biological_process	plasmacytoid dendritic cell activation
K	0002281	biological_process	macrophage activation involved in immune response
K	0002376	biological_process	immune system process
K	0002407	biological_process	dendritic cell chemotaxis
K	0002437	biological_process	inflammatory response to antigenic stimulus
K	0002643	biological_process	regulation of tolerance induction
K	0002840	biological_process	regulation of T cell mediated immune response to tumor cell
K	0003677	molecular_function	DNA binding
K	0003684	molecular_function	damaged DNA binding
K	0003690	molecular_function	double-stranded DNA binding
K	0003697	molecular_function	single-stranded DNA binding
K	0003713	molecular_function	transcription coactivator activity
K	0003714	molecular_function	transcription corepressor activity
K	0003723	molecular_function	RNA binding
K	0003725	molecular_function	double-stranded RNA binding
K	0003727	molecular_function	single-stranded RNA binding
K	0005125	molecular_function	cytokine activity
K	0005178	molecular_function	integrin binding
K	0005515	molecular_function	protein binding
K	0005576	cellular_component	extracellular region
K	0005615	cellular_component	extracellular space
K	0005634	cellular_component	nucleus
K	0005654	cellular_component	nucleoplasm
K	0005694	cellular_component	chromosome
K	0005737	cellular_component	cytoplasm
K	0005768	cellular_component	endosome
K	0005769	cellular_component	early endosome
K	0005783	cellular_component	endoplasmic reticulum
K	0005793	cellular_component	endoplasmic reticulum-Golgi intermediate compartment
K	0005886	cellular_component	plasma membrane
K	0006259	biological_process	DNA metabolic process
K	0006265	biological_process	DNA topological change
K	0006281	biological_process	DNA repair
K	0006284	biological_process	base-excision repair
K	0006302	biological_process	double-strand break repair
K	0006303	biological_process	double-strand break repair via nonhomologous end joining
K	0006310	biological_process	DNA recombination
K	0006325	biological_process	chromatin organization
K	0006338	biological_process	chromatin remodeling
K	0006914	biological_process	autophagy
K	0006935	biological_process	chemotaxis
K	0006954	biological_process	inflammatory response
K	0006955	biological_process	immune response
K	0006974	biological_process	DNA damage response
K	0007165	biological_process	signal transduction
K	0007204	biological_process	positive regulation of cytosolic calcium ion concentration
K	0008289	molecular_function	lipid binding
K	0008301	molecular_function	DNA binding, bending
K	0009986	cellular_component	cell surface
K	0010508	biological_process	positive regulation of autophagy
K	0010596	biological_process	negative regulation of endothelial cell migration
K	0010858	molecular_function	calcium-dependent protein kinase regulator activity
K	0016829	molecular_function	lyase activity
K	0017053	cellular_component	transcription repressor complex
K	0017055	biological_process	negative regulation of RNA polymerase II transcription preinitiation complex assembly
K	0019958	molecular_function	C-X-C chemokine binding
K	0030295	molecular_function	protein kinase activator activity
K	0031175	biological_process	neuron projection development
K	0031507	biological_process	heterochromatin formation
K	0032392	biological_process	DNA geometric change
K	0032425	biological_process	positive regulation of mismatch repair
K	0032689	biological_process	negative regulation of type II interferon production
K	0032722	biological_process	positive regulation of chemokine production
K	0032727	biological_process	positive regulation of interferon-alpha production
K	0032728	biological_process	positive regulation of interferon-beta production
K	0032731	biological_process	positive regulation of interleukin-1 beta production
K	0032732	biological_process	positive regulation of interleukin-1 production
K	0032733	biological_process	positive regulation of interleukin-10 production
K	0032735	biological_process	positive regulation of interleukin-12 production
K	0032755	biological_process	positive regulation of interleukin-6 production
K	0032757	biological_process	positive regulation of interleukin-8 production
K	0032760	biological_process	positive regulation of tumor necrosis factor production
K	0033151	biological_process	V(D)J recombination
K	0034137	biological_process	positive regulation of toll-like receptor 2 signaling pathway
K	0034145	biological_process	positive regulation of toll-like receptor 4 signaling pathway
K	0034165	biological_process	positive regulation of toll-like receptor 9 signaling pathway
K	0034774	cellular_component	secretory granule lumen
K	0035711	biological_process	T-helper 1 cell activation
K	0035767	biological_process	endothelial cell chemotaxis
K	0035868	cellular_component	alphav-beta3 integrin-HMGB1 complex
K	0042056	molecular_function	chemoattractant activity
K	0042104	biological_process	positive regulation of activated T cell proliferation
K	0043005	cellular_component	neuron projection
K	0043065	biological_process	positive regulation of apoptotic process
K	0043277	biological_process	apoptotic cell clearance
K	0043371	biological_process	negative regulation of CD4-positive, alpha-beta T cell differentiation
K	0043388	biological_process	positive regulation of DNA binding
K	0043410	biological_process	positive regulation of MAPK cascade
K	0043536	biological_process	positive regulation of blood vessel endothelial cell migration
K	0043537	biological_process	negative regulation of blood vessel endothelial cell migration
K	0045063	biological_process	T-helper 1 cell differentiation
K	0045087	biological_process	innate immune response
K	0045089	biological_process	positive regulation of innate immune response
K	0045597	biological_process	positive regulation of cell differentiation
K	0045944	biological_process	positive regulation of transcription by RNA polymerase II
K	0046330	biological_process	positive regulation of JNK cascade
K	0046598	biological_process	positive regulation of viral entry into host cell
K	0048018	molecular_function	receptor ligand activity
K	0048468	biological_process	cell development
K	0050786	molecular_function	RAGE receptor binding
K	0050792	biological_process	regulation of viral process
K	0050918	biological_process	positive chemotaxis
K	0051052	biological_process	regulation of DNA metabolic process
K	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
K	0070182	molecular_function	DNA polymerase binding
K	0070374	biological_process	positive regulation of ERK1 and ERK2 cascade
K	0071222	biological_process	cellular response to lipopolysaccharide
K	0071639	biological_process	positive regulation of monocyte chemotactic protein-1 production
K	0090026	biological_process	positive regulation of monocyte chemotaxis
K	0090303	biological_process	positive regulation of wound healing
K	0097100	molecular_function	supercoiled DNA binding
K	0097350	biological_process	neutrophil clearance
K	0140297	molecular_function	DNA-binding transcription factor binding
K	0140656	molecular_function	endodeoxyribonuclease activator activity
K	1901224	biological_process	positive regulation of non-canonical NF-kappaB signal transduction
K	1903672	biological_process	positive regulation of sprouting angiogenesis
K	1903706	biological_process	regulation of hemopoiesis
K	1904813	cellular_component	ficolin-1-rich granule lumen
K	1905564	biological_process	positive regulation of vascular endothelial cell proliferation
K	2000343	biological_process	positive regulation of chemokine (C-X-C motif) ligand 2 production
K	2000426	biological_process	negative regulation of apoptotic cell clearance
K	2000819	biological_process	regulation of nucleotide-excision repair
K	2001200	biological_process	positive regulation of dendritic cell differentiation

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	PS00353
Number of Residues	12
Details	HMG_BOX_1 HMG box A DNA-binding domain signature. FSKKCsERWKTM

Chain	Residue	Details
K	PHE40-MET51

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	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P68431","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
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_FI4
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	2
Details	Modified residue: {"description":"N6-methyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"Q71DI3","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P84243","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
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_FI9
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_FI10
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_FI11
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_FI12
Number of Residues	4
Details	Modified residue: {"description":"N6-propionyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
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_FI14
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
Details	Modified residue: {"description":"N6-methacryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P62805","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
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_FI17
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_FI18
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

site_id	SWS_FT_FI19
Number of Residues	2
Details	Modified residue: {"description":"N6-benzoyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	2
Details	Modified residue: {"description":"N6-isonicotinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	2
Details	Modified residue: {"description":"N6-benzoyllysine; alternate","evidences":[{"source":"UniProtKB","id":"C0HKE1","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
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_FI23
Number of Residues	2
Details	Modified residue: {"description":"N6-succinyllysine","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	2
Details	Modified residue: {"description":"N5-methylglutamine","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	2
Details	Modified residue: {"description":"N6-glutaryllysine; alternate","evidences":[{"source":"UniProtKB","id":"P0C0S8","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	6
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_FI27
Number of Residues	4
Details	Modified residue: {"description":"N6-isonicotinyllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q93079","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI28
Number of Residues	6
Details	Modified residue: {"description":"N6-methacryllysine; alternate","evidences":[{"source":"UniProtKB","id":"Q93079","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI29
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_FI30
Number of Residues	4
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"UniProtKB","id":"P0C1H4","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI31
Number of Residues	1
Details	Site: {"description":"Cleavage; by CASP1","evidences":[{"source":"PubMed","id":"24474694","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI32
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P10103","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI33
Number of Residues	2
Details	Modified residue: {"description":"Cysteine sulfonic acid (-SO3H); alternate","evidences":[{"source":"UniProtKB","id":"P63159","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI34
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI35
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P63158","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI36
Number of Residues	5
Details	Cross-link: {"description":"Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-?)","evidences":[{"source":"PubMed","id":"29618516","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

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