Structure of PDB 8ybk Chain D

Receptor sequence
>8ybkD (length=95) Species: 9606 (Homo sapiens) [Search protein sequence]
RSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASRL
AHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK
3D structure
PDB8ybk Cryo-EM structure and biochemical analyses of the nucleosome containing the cancer-associated histone H3 mutation E97K.
ChainD
Resolution2.69 Å
3D
structure
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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 R31 S56 R86 S87 T88 R1 S26 R56 S57 T58
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8ybk, PDBe:8ybk, PDBj:8ybk
PDBsum8ybk
PubMed38972377
UniProtP06899|H2B1J_HUMAN Histone H2B type 1-J (Gene Name=H2BC11)

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