Structure of PDB 8ybj Chain D

Receptor sequence

>8ybjD (length=92) Species: 9606 (Homo sapiens) [Search protein sequence]

RKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRLAH
YNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSA

3D structure

PDB

8ybj Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K.

Chain

Resolution

2.38 Å

3D
structure

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	dna	D	Y42 I54 S56 R86 S87 T88	Y10 I22 S24 R54 S55 T56
BS02	dna	D	R33 I39 Y40	R1 I7 Y8

Gene Ontology

	Molecular Function
GO:0001530	lipopolysaccharide binding
GO:0003677	DNA binding
GO:0005515	protein binding

	Biological Process
GO:0002227	innate immune response in mucosa
GO:0006325	chromatin organization
GO:0006334	nucleosome assembly
GO:0010804	negative regulation of tumor necrosis factor-mediated signaling pathway
GO:0019731	antibacterial humoral response
GO:0031640	killing of cells of another organism
GO:0042742	defense response to bacterium
GO:0050829	defense response to Gram-negative bacterium
GO:0050830	defense response to Gram-positive bacterium
GO:0061644	protein localization to CENP-A containing chromatin
GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide

	Cellular Component
GO:0000786	nucleosome
GO:0005615	extracellular space
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005694	chromosome
GO:0005829	cytosol
GO:0005886	plasma membrane
GO:0043505	CENP-A containing nucleosome

External links

PDB	RCSB:8ybj, PDBe:8ybj, PDBj:8ybj
PDBsum	8ybj
PubMed	38972377
UniProt	P06899\|H2B1J_HUMAN Histone H2B type 1-J (Gene Name=H2BC11)