Structure of PDB 8smz Chain H

Receptor sequence

>8smzH (length=93) Species: 9606 (Homo sapiens)

RSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRL
AHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS

3D structure

• PDB: 8smz Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A. No density for Ub.) (Class 4)
• Chain: H
• Resolution: 3.2 Å

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	H	Y42 I54 S55 S87 T88	Y12 I24 S25 S57 T58

Gene Ontology

Molecular Function

• GO:0001530 lipopolysaccharide binding
• GO:0003677 DNA binding
• GO:0005515 protein binding
• GO:0030527 structural constituent of chromatin
• GO:0046982 protein heterodimerization activity

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:8smz, PDBe:8smz, PDBj:8smz
• PDBsum: 8smz
• PubMed: 38242129
• UniProt: P06899|H2B1J_HUMAN Histone H2B type 1-J (Gene Name=H2BC11)