Structure of PDB 8sn5 Chain D

Receptor sequence
>8sn5D (length=94) Species: 9606 (Homo sapiens) [Search protein sequence]
KRSRKESYSIYVYKVLKQVHPDTGISSKAMGIMNSFVNDIFERIAGEASR
LAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
3D structure
PDB8sn5 Cryo-EM structure of the human nucleosome core particle in complex with RNF168 and UbcH5c~Ub (UbcH5c chemically conjugated to histone H2A) (class 3)
ChainD
Resolution3.9 Å
3D
structure
[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]
Enzymatic activity
Enzyme Commision number ?
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 S32 Y42 I54 S56 R86 S3 Y13 I25 S27 R57
BS02 dna D R33 K34 Y40 R4 K5 Y11
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8sn5, PDBe:8sn5, PDBj:8sn5
PDBsum8sn5
PubMed38242129
UniProtP06899|H2B1J_HUMAN Histone H2B type 1-J (Gene Name=H2BC11)

[Back to BioLiP]